Repository: connectomicslab/connectomemapper3 (language: python)

Issue:
BUG: Unable to create environment from .yml in Ubuntu 20.04
Hi everyone,

I've been struggling for days trying to create the conda environment using the provided .yml file, but I get way too many conflicts and at the end it fails (I follow the instruction exactly as written in the docs: https://connectome-mapper-3.readthedocs.io/en/latest/installation.html)
CMP3 version: v3.0.1

I've already tried adjusting the channel priority in conda, change versions of the incompatible dependencies, re-installing conda altogether etc. none of them worked.
Could it be because of my Ubuntu version?

Logs:
1. This is the error i get when I run: `$ conda env create -f conda/environment.yml`

> collecting package metadata (repodata.json): - WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
> WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.*, but conda is ignoring the .* and treating it as 1
> / WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6.*, but conda is ignoring the .* and treating it as 3.6
> done
> Solving environment: /

And this takes forever.

2. When I set the conda channel priority to strict (conda-forge as priority) it goes one step further into solving the conflicts but still takes forever and crashes at the end. Here's the log:
 `$ conda env create -f conda/environment.yml`
> Collecting package metadata (repodata.json): - WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
> WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.*, but conda is ignoring the .* and treating it as 1
> / WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6.*, but conda is ignoring the .* and treating it as 3.6
> done
> Solving environment: / 
> Found conflicts! Looking for incompatible packages.
> This can take several minutes.  Press CTRL-C to abort.
> 

3. One solution worked half-way: I manually installed all dependencies with the specified versions. This way I could create the environment and activate it, then installed cmpbidsappmanager, but then I cannot launch the interface, I get an inconsistency issue between h5py and hdf5. Here is the log:
 `$ cmpbidsappmanager`
> (py37cmp-gui) fateme@fateme-HP:~/connectomemapper3$ cmpbidsappmanager
> Traceback (most recent call last):
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/bin/cmpbidsappmanager", line 5, in <module>
>     from cmp.cli.cmpbidsappmanager import main
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/cli/cmpbidsappmanager.py", line 21, in <module>
>     import cmp.bidsappmanager.gui.principal
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/bidsappmanager/gui/principal.py", line 21, in <module>
>     import cmp.project
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/project.py", line 23, in <module>
>     from cmp.pipelines.diffusion import diffusion as Diffusion_pipeline
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/pipelines/diffusion/diffusion.py", line 22, in <module>
>     from cmp.stages.diffusion.diffusion import DiffusionStage
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/diffusion.py", line 18, in <module>
>     from .reconstruction import *
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/reconstruction.py", line 34, in <module>
>     from cmtklib.interfaces.dipy import DTIEstimateResponseSH, CSD, SHORE, MAPMRI
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmtklib/interfaces/dipy.py", line 16, in <module>
>     from nipype.interfaces.dipy.base import DipyDiffusionInterface, DipyBaseInterface, DipyBaseInterfaceInputSpec
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/dipy/__init__.py", line 3, in <module>
>     from .tracks import StreamlineTractography, TrackDensityMap
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/dipy/tracks.py", line 34, in <module>
>     from dipy.workflows import segment, tracking
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/dipy/workflows/segment.py", line 4, in <module>
>     from dipy.io.image import save_nifti, load_nifti
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/dipy/io/__init__.py", line 4, in <module>
>     from .dpy import Dpy
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/dipy/io/dpy.py", line 12, in <module>
>     import h5py
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/h5py/__init__.py", line 33, in <module>
>     from . import version
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/h5py/version.py", line 15, in <module>
>     from . import h5 as _h5
>   File "h5py/h5.pyx", line 1, in init h5py.h5
> ImportError: /home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/h5py/defs.cpython-37m-x86_64-linux-gnu.so: undefined symbol: H5Pset_fapl_ros3
> 

Thanks!
Fatemeh
BUG: Unable to create environment from .yml in Ubuntu 20.04
Hi everyone,

I've been struggling for days trying to create the conda environment using the provided .yml file, but I get way too many conflicts and at the end it fails (I follow the instruction exactly as written in the docs: https://connectome-mapper-3.readthedocs.io/en/latest/installation.html)
CMP3 version: v3.0.1

I've already tried adjusting the channel priority in conda, change versions of the incompatible dependencies, re-installing conda altogether etc. none of them worked.
Could it be because of my Ubuntu version?

Logs:
1. This is the error i get when I run: `$ conda env create -f conda/environment.yml`

> collecting package metadata (repodata.json): - WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
> WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.*, but conda is ignoring the .* and treating it as 1
> / WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6.*, but conda is ignoring the .* and treating it as 3.6
> done
> Solving environment: /

And this takes forever.

2. When I set the conda channel priority to strict (conda-forge as priority) it goes one step further into solving the conflicts but still takes forever and crashes at the end. Here's the log:
 `$ conda env create -f conda/environment.yml`
> Collecting package metadata (repodata.json): - WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2.*, but conda is ignoring the .* and treating it as 2
> WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.*, but conda is ignoring the .* and treating it as 1
> / WARNING conda.models.version:get_matcher(540): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6.*, but conda is ignoring the .* and treating it as 3.6
> done
> Solving environment: / 
> Found conflicts! Looking for incompatible packages.
> This can take several minutes.  Press CTRL-C to abort.
> 

3. One solution worked half-way: I manually installed all dependencies with the specified versions. This way I could create the environment and activate it, then installed cmpbidsappmanager, but then I cannot launch the interface, I get an inconsistency issue between h5py and hdf5. Here is the log:
 `$ cmpbidsappmanager`
> (py37cmp-gui) fateme@fateme-HP:~/connectomemapper3$ cmpbidsappmanager
> Traceback (most recent call last):
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/bin/cmpbidsappmanager", line 5, in <module>
>     from cmp.cli.cmpbidsappmanager import main
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/cli/cmpbidsappmanager.py", line 21, in <module>
>     import cmp.bidsappmanager.gui.principal
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/bidsappmanager/gui/principal.py", line 21, in <module>
>     import cmp.project
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/project.py", line 23, in <module>
>     from cmp.pipelines.diffusion import diffusion as Diffusion_pipeline
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/pipelines/diffusion/diffusion.py", line 22, in <module>
>     from cmp.stages.diffusion.diffusion import DiffusionStage
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/diffusion.py", line 18, in <module>
>     from .reconstruction import *
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/stages/diffusion/reconstruction.py", line 34, in <module>
>     from cmtklib.interfaces.dipy import DTIEstimateResponseSH, CSD, SHORE, MAPMRI
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmtklib/interfaces/dipy.py", line 16, in <module>
>     from nipype.interfaces.dipy.base import DipyDiffusionInterface, DipyBaseInterface, DipyBaseInterfaceInputSpec
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/dipy/__init__.py", line 3, in <module>
>     from .tracks import StreamlineTractography, TrackDensityMap
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/dipy/tracks.py", line 34, in <module>
>     from dipy.workflows import segment, tracking
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/dipy/workflows/segment.py", line 4, in <module>
>     from dipy.io.image import save_nifti, load_nifti
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/dipy/io/__init__.py", line 4, in <module>
>     from .dpy import Dpy
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/dipy/io/dpy.py", line 12, in <module>
>     import h5py
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/h5py/__init__.py", line 33, in <module>
>     from . import version
>   File "/home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/h5py/version.py", line 15, in <module>
>     from . import h5 as _h5
>   File "h5py/h5.pyx", line 1, in init h5py.h5
> ImportError: /home/fateme/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/h5py/defs.cpython-37m-x86_64-linux-gnu.so: undefined symbol: H5Pset_fapl_ros3
> 

Thanks!
Fatemeh


Discussion / hints:

Fix patch:
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1040ed386..68f94dcb7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -166,11 +166,14 @@ commands:
                 --fs_license "${bids_dir}/code/license.txt" \
                 --ants_number_of_threads 4 \
                 --coverage \
-                --notrack
+                --notrack \
+                --track_carbon_footprint
             # Rename partial coverage
             mv /tmp/data/<<parameters.circleci_job>>/ds-sample/code/coverage.xml /tmp/data/ds-sample/test/<<parameters.test_name>>_coverage.xml
             # Rename execution log
             mv /tmp/data/<<parameters.circleci_job>>/ds-sample/code/log.txt /tmp/data/ds-sample/test/<<parameters.test_name>>_log.txt
+            # Rename emissions log
+            mv /tmp/data/<<parameters.circleci_job>>/ds-sample/code/emissions.csv /tmp/data/ds-sample/test/<<parameters.test_name>>_co2emissions.csv
       - run:
           name: Checking outputs of Connectome Mapper run (<<parameters.test_name>>)
           command: |
@@ -220,11 +223,14 @@ commands:
                 --fs_license "${bids_dir}/code/license.txt" \
                 --ants_number_of_threads 4 \
                 --coverage \
-                --notrack
+                --notrack \
+                --track_carbon_footprint
             # Rename partial coverage
             mv /tmp/data/<<parameters.circleci_job>>/ds-sample/code/coverage.xml /tmp/data/ds-sample/test/<<parameters.test_name>>_coverage.xml
             # Rename execution log
             mv /tmp/data/<<parameters.circleci_job>>/ds-sample/code/log.txt /tmp/data/ds-sample/test/<<parameters.test_name>>_log.txt
+            # Rename emissions log
+            mv /tmp/data/<<parameters.circleci_job>>/ds-sample/code/emissions.csv /tmp/data/ds-sample/test/<<parameters.test_name>>_co2emissions.csv
       - run:
           name: Checking outputs of Connectome Mapper run (<<parameters.test_name>>)
           command: |
diff --git a/.zenodo.json b/.zenodo.json
index e4f67d3cf..d0eec6612 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -32,15 +32,20 @@
         "orcid": "0000-0003-1923-1653"
       },
       {
-        "name": "Jonathan Wirsich",
+        "name": "Wirsich, Jonathan",
         "affiliation": "Departement des Neurosciences Cliniques, University of Geneva, Switzerland",
         "orcid": "0000-0003-0588-9710"
       },
       {
-        "name": "Anil Tuncel",
+        "name": "Tuncel, Anil",
         "affiliation": "Blue Brain Project, BBP-CORE, Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland",
         "orcid": "0000-0003-0317-2556"
       },
+      {
+        "name": "Jancovic, Jakub",
+        "affiliation": "Foxight, Geneva, Switzerland",
+        "orcid": "0000-0002-3312-3918"
+      },
       {
         "name": "Bach Cuadra, Meritxell",
         "affiliation": "Department of Radiology, Lausanne University Hospital (CHUV), Switzerland",
diff --git a/cmp/bidsappmanager/gui/bidsapp.py b/cmp/bidsappmanager/gui/bidsapp.py
index d856887ee..6f363c5c8 100644
--- a/cmp/bidsappmanager/gui/bidsapp.py
+++ b/cmp/bidsappmanager/gui/bidsapp.py
@@ -9,6 +9,7 @@
 # General imports
 import os
 import sys
+import logging
 
 import pkg_resources
 from subprocess import Popen
@@ -17,7 +18,9 @@
 import shutil
 import time
 import glob
+from pathlib import Path
 
+from codecarbon import EmissionsTracker
 from pyface.api import ImageResource
 from traitsui.qt4.extra.qt_view import QtView
 from traitsui.api import *
@@ -39,11 +42,15 @@
     print_warning,
     print_error,
 )
+from cmtklib.carbonfootprint import (
+    create_emissions_tracker,
+    create_html_carbon_footprint_report, create_carbon_footprint_message
+)
 
 import cmp.bidsappmanager.gui.handlers
 import cmp.bidsappmanager.project as project
 from cmp.bidsappmanager.gui.traits import MultiSelectAdapter
-from cmp.bidsappmanager.gui.globals import get_icon
+from cmp.bidsappmanager.gui.globals import get_icon, modal_width
 
 # Remove warnings visible whenever you import scipy (or another package)
 # that was compiled against an older numpy than is installed.
@@ -127,6 +134,12 @@ class BIDSAppInterfaceWindow(HasTraits):
         Boolean used to store if datalad is available in the computing
         environment (False by default)
 
+    track_carbon_footprint : traits.Bool
+        Track carbon footprint if `True` (True by default)
+
+    carbon_emission_msg : traits.Str
+        Carbon footprint reporting message
+
     check : traits.ui.Button
         Button to check if all parameters are properly set for execution
         of the BIDS App
@@ -214,28 +227,42 @@ class BIDSAppInterfaceWindow(HasTraits):
 
     datalad_is_available = Bool(False, desc="True if datalad is available")
 
+    track_carbon_footprint = Bool(
+        True,
+        desc="Track carbon footprint with `codecarbon <https://codecarbon.io/>`_, and save results in "
+             "a CSV file called ``emissions.csv`` in the ``<bids_dir>/code`` directory."
+    )
+
+    carbon_emission_msg = Str('Results not yet available!')
+
     update_selection = Button()
     check = Button()
     start_bidsapp = Button()
-
-    # stop_bidsapp = Action(name='Stop BIDS App!',action='stop_bids_app',enabled_when='handler.settings_checked and handler.docker_running')
+    # stop_bidsapp = Button()
 
     traits_view = QtView(
         Group(
             VGroup(
                 VGroup(
-                        Item("bidsapp_tag", style="readonly", label="Tag"),
-                        label="BIDS App Version",
+                    Item("bidsapp_tag", style="readonly", label="Tag"),
+                    label="BIDS App Version",
+                ),
+                HGroup(
+                    Item(
+                        "track_carbon_footprint",
+                        label="Track carbon footprint",
+                    ),
+                    label="Environmental impact",
                 ),
                 VGroup(
-                        Item("bids_root", style="readonly", label="Input directory"),
-                        Item(
-                                "output_dir",
-                                style="simple",
-                                label="Output directory",
-                                enabled_when="not(data_provenance_tracking)",
-                        ),
-                        label="BIDS dataset",
+                    Item("bids_root", style="readonly", label="Input directory"),
+                    Item(
+                        "output_dir",
+                        style="simple",
+                        label="Output directory",
+                        enabled_when="not(data_provenance_tracking)",
+                    ),
+                    label="BIDS dataset",
                 ),
                 VGroup(
                     HGroup(
@@ -350,7 +377,6 @@ class BIDSAppInterfaceWindow(HasTraits):
                         editor=FileEditor(dialog_style="open"),
                         label="LICENSE",
                     ),
-                    # Item('fs_average', label='FSaverage directory'),
                     label="Freesurfer configuration",
                 ),
                 VGroup(
@@ -368,63 +394,58 @@ class BIDSAppInterfaceWindow(HasTraits):
             ),
             spring,
             HGroup(
-                    spring,
-                    Item(
-                            "check",
-                            style="custom",
-                            width=152,
-                            height=35,
-                            resizable=False,
-                            label="",
-                            show_label=False,
-                            style_sheet=return_button_style_sheet(
-                                    ImageResource(
-                                            pkg_resources.resource_filename(
-                                                    "resources",
-                                                    os.path.join("buttons", "bidsapp-check-settings.png"),
-                                            )
-                                    ).absolute_path
-                            ),
-                    ),
-                    spring,
-                    Item(
-                            "start_bidsapp",
-                            style="custom",
-                            width=152,
-                            height=35,
-                            resizable=False,
-                            label="",
-                            show_label=False,
-                            style_sheet=return_button_style_sheet(
-                                    ImageResource(
-                                            pkg_resources.resource_filename(
-                                                    "resources", os.path.join("buttons", "bidsapp-run.png")
-                                            )
-                                    ).absolute_path,
-                                    ImageResource(
-                                            pkg_resources.resource_filename(
-                                                    "resources",
-                                                    os.path.join("buttons", "bidsapp-run-disabled.png"),
-                                            )
-                                    ).absolute_path,
-                            ),
-                            enabled_when="settings_checked==True and docker_running==False",
+                spring,
+                Item(
+                    "check",
+                    style="custom",
+                    width=152,
+                    height=35,
+                    resizable=False,
+                    label="",
+                    show_label=False,
+                    style_sheet=return_button_style_sheet(
+                        ImageResource(
+                            pkg_resources.resource_filename(
+                                "resources",
+                                os.path.join("buttons", "bidsapp-check-settings.png"),
+                            )
+                        ).absolute_path
                     ),
-                    spring,
-                    show_labels=False,
+                ),
+                spring,
+                Item(
+                    "start_bidsapp",
+                    style="custom",
+                    width=152,
+                    height=35,
+                    resizable=False,
                     label="",
+                    show_label=False,
+                    style_sheet=return_button_style_sheet(
+                        ImageResource(
+                            pkg_resources.resource_filename(
+                                "resources", os.path.join("buttons", "bidsapp-run.png")
+                            )
+                        ).absolute_path,
+                        ImageResource(
+                            pkg_resources.resource_filename(
+                                "resources",
+                                os.path.join("buttons", "bidsapp-run-disabled.png"),
+                            )
+                        ).absolute_path,
+                    ),
+                    enabled_when="settings_checked==True and docker_running==False",
+                ),
+                spring,
+                show_labels=False,
+                label="",
             ),
             orientation="vertical",
             springy=True,
         ),
         title="Connectome Mapper 3 BIDS App GUI",
-        # kind='modal',
         handler=cmp.bidsappmanager.gui.handlers.BIDSAppInterfaceWindowHandler(),
-        # style_sheet=style_sheet,
         buttons=[],
-        # buttons = [check,start_bidsapp],
-        # buttons = [process_anatomical,map_dmri_connectome,map_fmri_connectome],
-        # buttons = [preprocessing, map_connectome, map_custom],
         width=0.6,
         height=0.8,
         scrollable=True,  # , resizable=True
@@ -432,32 +453,39 @@ class BIDSAppInterfaceWindow(HasTraits):
     )
 
     log_view = QtView(
-            Group(
-                    Item("list_of_processing_logfiles"), orientation="vertical", springy=True
-            ),
-            title="Connectome Mapper 3 BIDS App Progress",
-            # kind='modal',
-            # handler=project.BIDSAppInterfaceWindowHandler(),
-            # style_sheet=style_sheet,
-            buttons=[],
-            # buttons = [check,start_bidsapp],
-            # buttons = [process_anatomical,map_dmri_connectome,map_fmri_connectome],
-            # buttons = [preprocessing, map_connectome, map_custom],
-            width=0.5,
-            height=0.8,
-            resizable=True,  # , scrollable=True, resizable=True
-            icon=get_icon("bidsapp.png"),
+        Group(
+           Item("list_of_processing_logfiles"), orientation="vertical", springy=True
+        ),
+        title="Connectome Mapper 3 BIDS App Progress",
+        buttons=[],
+        width=0.5,
+        height=0.8,
+        resizable=True,  # , scrollable=True, resizable=True
+        icon=get_icon("bidsapp.png"),
+    )
+
+    carbon_footprint_view = View(
+        Group(
+            Item("carbon_emission_msg", editor=HTMLEditor(), show_label=False),
+        ),
+        title="Carbon Footprint Report",
+        kind="modal",
+        width=2.2*modal_width,
+        height=770,
+        resizable=True,
+        scrollable=False,
+        buttons=["OK"],
     )
 
     def __init__(
-            self,
-            project_info=None,
-            bids_root="",
-            subjects=None,
-            list_of_subjects_to_be_processed=None,
-            anat_config="",
-            dmri_config="",
-            fmri_config="",
+        self,
+        project_info=None,
+        bids_root="",
+        subjects=None,
+        list_of_subjects_to_be_processed=None,
+        anat_config="",
+        dmri_config="",
+        fmri_config="",
     ):
         """Constructor of an :class:``BIDSAppInterfaceWindow`` instance.
 
@@ -500,7 +528,7 @@ def __init__(
 
         # Check if sMRI data is available in the dataset
         smri_files = bids_layout.get(
-                datatype="anat", suffix="T1w", extensions="nii.gz", return_type="file"
+            datatype="anat", suffix="T1w", extension="nii.gz", return_type="file"
         )
 
         if not smri_files:
@@ -512,7 +540,7 @@ def __init__(
 
         # Check if dMRI data is available in the dataset
         dmri_files = bids_layout.get(
-                datatype="dwi", suffix="dwi", extensions="nii.gz", return_type="file"
+            datatype="dwi", suffix="dwi", extension="nii.gz", return_type="file"
         )
 
         if not dmri_files:
@@ -526,11 +554,11 @@ def __init__(
 
         # Check if fMRI data is available in the dataset
         fmri_files = bids_layout.get(
-                task="rest",
-                datatype="func",
-                suffix="bold",
-                extensions="nii.gz",
-                return_type="file",
+            task="rest",
+            datatype="func",
+            suffix="bold",
+            extension="nii.gz",
+            return_type="file",
         )
         if not fmri_files:
             self.fmri_inputs_checked = False
@@ -567,12 +595,12 @@ def __init__(
         self.on_trait_change(self.update_run_fmri_pipeline, "run_fmri_pipeline")
 
         self.on_trait_change(
-                self.number_of_parallel_procs_updated,
-                "number_of_participants_processed_in_parallel",
+            self.number_of_parallel_procs_updated,
+            "number_of_participants_processed_in_parallel",
         )
 
         self.on_trait_change(
-                self.update_checksettings, "list_of_subjects_to_be_processed"
+            self.update_checksettings, "list_of_subjects_to_be_processed"
         )
         self.on_trait_change(self.update_checksettings, "anat_config")
         self.on_trait_change(self.update_checksettings, "run_dmri_pipeline")
@@ -580,7 +608,6 @@ def __init__(
         self.on_trait_change(self.update_checksettings, "run_fmri_pipeline")
         self.on_trait_change(self.update_checksettings, "fmri_config")
         self.on_trait_change(self.update_checksettings, "fs_license")
-        # self.on_trait_change(self.update_checksettings, 'fs_average')
 
     def number_of_parallel_procs_updated(self, new):
         """Callback function when ``number_of_parallel_procs`` is updated."""
@@ -590,12 +617,7 @@ def number_of_parallel_procs_updated(self, new):
             self.number_of_threads_max = 4
         else:
             self.number_of_threads_max = number_of_threads_max
-
-        print(
-                "  .. INFO : Update number of threads max to : {}".format(
-                        self.number_of_threads_max
-                )
-        )
+        print("  .. INFO : Update number of threads max to : {}".format(self.number_of_threads_max))
 
     def update_run_anat_pipeline(self, new):
         """Callback function when ``run_anat_pipeline`` is updated."""
@@ -655,23 +677,19 @@ def check_settings(self):
 
         if len(self.list_of_subjects_to_be_processed) > 0:
             print(
-                    f"* Participant labels to be processed : {self.list_of_subjects_to_be_processed}"
+                f"* Participant labels to be processed : {self.list_of_subjects_to_be_processed}"
             )
         else:
             print_error(
-                    "Error: At least one participant label to be processed should selected!"
+                "Error: At least one participant label to be processed should selected!"
             )
             self.settings_checked = False
-        # if not self.list_of_subjects_to_be_processed.empty():
-        #     print("List of subjects to be processed : {}".format(self.list_of_subjects_to_be_processed))
-        # else:
-        #     print("Warning: List of subjects empty!")
 
         if os.path.isfile(self.anat_config):
             print(f"* Anatomical configuration file : {self.anat_config}")
         else:
             print_error(
-                    "Error: Configuration file for anatomical pipeline not existing!"
+                "Error: Configuration file for anatomical pipeline not existing!"
             )
             self.settings_checked = False
 
@@ -679,7 +697,7 @@ def check_settings(self):
             print(f"* Diffusion configuration file : {self.dmri_config}")
         else:
             print_warning(
-                    "Warning: Configuration file for diffusion pipeline not existing!"
+                "Warning: Configuration file for diffusion pipeline not existing!"
             )
 
         if os.path.isfile(self.fmri_config):
@@ -693,39 +711,23 @@ def check_settings(self):
             print_error(f"Error: Invalid Freesurfer license ({self.fs_license})!")
             self.settings_checked = False
 
-        # if os.path.isdir(self.fs_average):
-        #     print("fsaverage directory : {}".format(self.fs_average))
-        # else:
-        #     print("Error: fsaverage directory ({}) not existing!".format(self.fs_average))
-        #     self.settings_checked = False
-
         print(f"Valid inputs for BIDS App : {self.settings_checked}")
         print(f"BIDS App Version Tag: {self.bidsapp_tag}")
         print(f"Data provenance tracking (datalad) : {self.data_provenance_tracking}")
+        print(f"Update computing environment (datalad) : {self.datalad_update_environment}")
         print(
-                f"Update computing environment (datalad) : {self.datalad_update_environment}"
-        )
-        print(
-                f"Number of participant processed in parallel : {self.number_of_participants_processed_in_parallel}"
+            f"Number of participant processed in parallel : {self.number_of_participants_processed_in_parallel}"
         )
         print(f"Number of OpenMP threads / participant : {self.number_of_threads}")
-
         print(f"Fix number of ITK threads : {self.fix_ants_number_of_threads}")
         if self.fix_ants_number_of_threads:
-            print(
-                    f"Number of ITK threads (ANTs) / participant : {self.ants_number_of_threads}"
-            )
-
+            print(f"Number of ITK threads (ANTs) / participant : {self.ants_number_of_threads}")
         print(f"Fix seed in ANTS random number generator : {self.fix_ants_random_seed}")
         if self.fix_ants_random_seed:
             print(f"Seed value : {self.ants_random_seed}")
-
-        print(
-                f"Fix seed in MRtrix random number generator : {self.fix_mrtrix_random_seed}"
-        )
+        print(f"Fix seed in MRtrix random number generator : {self.fix_mrtrix_random_seed}")
         if self.fix_ants_random_seed:
             print(f"Seed value : {self.mrtrix_random_seed}")
-
         print("-----------------------------------------\n")
 
         return True
@@ -742,20 +744,15 @@ def start_bidsapp_participant_level_process(self, bidsapp_tag, participant_label
             List of participants labels in the form ["01", "03", "04", ...]
         """
 
+        # fmt: off
         cmd = [
-                "docker",
-                "run",
-                "-it",
-                "--rm",
-                "-v",
-                "{}:/bids_dir".format(self.bids_root),
-                "-v",
-                "{}:/output_dir".format(self.output_dir),
-                "-v",
-                "{}:/bids_dir/code/license.txt".format(self.fs_license),
-                "-v",
-                "{}:/code/ref_anatomical_config.json".format(self.anat_config),
+            "docker", "run", "-it", "--rm",
+            "-v", "{}:/bids_dir".format(self.bids_root),
+            "-v", "{}:/output_dir".format(self.output_dir),
+            "-v", "{}:/bids_dir/code/license.txt".format(self.fs_license),
+            "-v", "{}:/code/ref_anatomical_config.json".format(self.anat_config),
         ]
+        # fmt: on
 
         if self.run_dmri_pipeline:
             cmd.append("-v")
@@ -812,7 +809,6 @@ def start_bidsapp_participant_level_process(self, bidsapp_tag, participant_label
         print_blue("... BIDS App execution command: {}".format(" ".join(cmd)))
 
         proc = Popen(cmd)
-        # proc = Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
         return proc
 
@@ -829,31 +825,16 @@ def start_bidsapp_participant_level_process_with_datalad(
         participant_labels : traits.List
             List of participants labels in the form ["01", "03", "04", ...]
         """
+        # fmt: off
         cmd = [
-                "datalad",
-                "containers-run",
-                "--container-name",
-                "connectomemapper-bidsapp-{}".format("-".join(bidsapp_tag.split("."))),
-                "-m",
-                "Processing with connectomemapper-bidsapp {}".format(bidsapp_tag),
-                "--input",
-                f"{self.anat_config}",
+                "datalad", "containers-run",
+                "--container-name", "connectomemapper-bidsapp-{}".format(
+                    "-".join(bidsapp_tag.split("."))
+                ),
+                "-m", "Processing with connectomemapper-bidsapp {}".format(bidsapp_tag),
+                "--input", f"{self.anat_config}",
         ]
-
-        # for label in participant_labels:
-        #     cmd.append('--input')
-        #     cmd.append('sub-{}/ses-*/anat/sub-*_T1w.*'.format(label))
-        #
-        #     cmd.append('--input')
-        #     cmd.append('derivatives/freesurfer/sub-{}*/*'.format(label))
-        #
-        #     if self.run_dmri_pipeline:
-        #         cmd.append('--input')
-        #         cmd.append('sub-{}/ses-*/dwi/sub-*_dwi.*'.format(label))
-        #
-        #     if self.run_fmri_pipeline:
-        #         cmd.append('--input')
-        #         cmd.append('sub-{}/ses-*/func/sub-*_bold.*'.format(label))
+        # fmt: on
 
         if self.run_dmri_pipeline:
             cmd.append("--input")
@@ -865,10 +846,6 @@ def start_bidsapp_participant_level_process_with_datalad(
 
         cmd.append("--output")
         cmd.append(f"{self.output_dir}")
-        # for label in participant_labels:
-        #     cmd.append('--input')
-        #     cmd.append('{}'.format(label))
-
         cmd.append("/bids_dir")
         cmd.append("/output_dir")
         cmd.append("participant")
@@ -894,12 +871,11 @@ def start_bidsapp_participant_level_process_with_datalad(
         print_blue("... Datalad cmd : {}".format(" ".join(cmd)))
 
         proc = Popen(cmd, cwd=os.path.join(self.bids_root))
-        # proc = Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=os.path.join(self.bids_root,'derivatives'))
 
         return proc
 
     @classmethod
-    def manage_bidsapp_procs(self, proclist):
+    def manage_bidsapp_procs(cls, proclist):
         """Manage parallelized process at the participant level
 
         Parameters
@@ -912,7 +888,7 @@ def manage_bidsapp_procs(self, proclist):
                 proclist.remove(proc)
 
     @classmethod
-    def run(self, command, env=None, cwd=os.getcwd()):
+    def run(cls, command, env=None, cwd=os.getcwd()):
         """Function to run datalad commands.
 
         It runs the command specified as input via ``subprocess.run()``.
@@ -1083,53 +1059,45 @@ def start_bids_app(self):
                 # Define the docker run command executed by Datalad.
                 # It makes the assumption that the license.txt and the configuration files
                 # are located in the code/ directory.
+                # fmt: off
                 docker_cmd = [
-                        "docker",
-                        "run",
-                        "--rm",
-                        "-t",
-                        "-v",
-                        '"$(pwd)":/bids_dir',
-                        "-v",
-                        '"$(pwd)"/derivatives:/output_dir',
-                        "-v",
-                        '"$(pwd)"/code/license.txt:/bids_dir/code/license.txt',
-                        "-v",
-                        f'"$(pwd)"/code/{os.path.basename(self.anat_config)}:/code/ref_anatomical_config.json',
+                    "docker", "run", "--rm", "-t",
+                    "-v", '"$(pwd)":/bids_dir',
+                    "-v", '"$(pwd)"/derivatives:/output_dir',
+                    "-v", '"$(pwd)"/code/license.txt:/bids_dir/code/license.txt',
+                    "-v", f'"$(pwd)"/code/{os.path.basename(self.anat_config)}:/code/ref_anatomical_config.json',
                 ]
+                # fmt: on
 
                 if self.run_dmri_pipeline:
                     docker_cmd.append("-v")
                     docker_cmd.append(
-                            f'"$(pwd)"/code/{os.path.basename(self.dmri_config)}:/code/ref_diffusion_config.json'
+                        f'"$(pwd)"/code/{os.path.basename(self.dmri_config)}:/code/ref_diffusion_config.json'
                     )
 
                 if self.run_fmri_pipeline:
                     docker_cmd.append("-v")
                     docker_cmd.append(
-                            f'"$(pwd)"/code/{os.path.basename(self.fmri_config)}:/code/ref_fMRI_config.json'
+                        f'"$(pwd)"/code/{os.path.basename(self.fmri_config)}:/code/ref_fMRI_config.json'
                     )
 
                 docker_cmd.append("-u")
                 docker_cmd.append("{}:{}".format(os.geteuid(), os.getegid()))
 
-                docker_cmd.append(
-                        f"sebastientourbier/connectomemapper-bidsapp:{self.bidsapp_tag}"
-                )
+                docker_cmd.append(f"sebastientourbier/connectomemapper-bidsapp:{self.bidsapp_tag}")
                 docker_cmd.append("{cmd}")
 
                 # Define and run the command to add the container image to datalad
                 version_tag = "-".join(self.bidsapp_tag.split("."))
+                # fmt: off
                 cmd = [
-                        "datalad",
-                        "containers-add",
-                        f"connectomemapper-bidsapp-{version_tag}",
-                        "--url",
-                        f"dhub://sebastientourbier/connectomemapper-bidsapp:{self.bidsapp_tag}",
-                        "-d",
-                        ".",
-                        "--call-fmt",
+                    "datalad", "containers-add",
+                    f"connectomemapper-bidsapp-{version_tag}",
+                    "--url", f"dhub://sebastientourbier/connectomemapper-bidsapp:{self.bidsapp_tag}",
+                    "-d", ".",
+                    "--call-fmt",
                 ]
+                # fmt: on
 
                 cmd = " ".join(cmd)
                 docker_cmd = " ".join(docker_cmd)
@@ -1140,13 +1108,9 @@ def start_bids_app(self):
                 try:
                     print_blue(f"... cmd: {cmd}")
                     self.run(cmd, env={}, cwd=os.path.join(self.bids_root))
-                    print(
-                            "    INFO: Container image has been linked to dataset with success!"
-                    )
+                    print("    INFO: Container image has been linked to dataset with success!")
                 except Exception:
-                    print_error(
-                            "   DATALAD ERROR: Failed to link the container image to the dataset"
-                    )
+                    print_error("   DATALAD ERROR: Failed to link the container image to the dataset")
 
             # Create a list of files to be retrieved by datalad get
             datalad_get_list = [self.anat_config]
@@ -1160,64 +1124,62 @@ def start_bids_app(self):
             if session_structure:
                 for label in self.list_of_subjects_to_be_processed:
                     datalad_get_list.append(
-                            "sub-{}/ses-*/anat/sub-{}*_T1w.*".format(label, label)
+                        "sub-{}/ses-*/anat/sub-{}*_T1w.*".format(label, label)
                     )
                     datalad_get_list.append(
-                            "derivatives/{}/sub-{}*/*".format(__freesurfer_directory__, label)
+                        "derivatives/{}/sub-{}*/*".format(__freesurfer_directory__, label)
                     )
                     if self.run_dmri_pipeline:
                         datalad_get_list.append(
-                                "sub-{}/ses-*/dwi/sub-{}*_dwi.*".format(label, label)
+                            "sub-{}/ses-*/dwi/sub-{}*_dwi.*".format(label, label)
                         )
                     if self.run_fmri_pipeline:
                         datalad_get_list.append(
-                                "sub-{}/ses-*/func/sub-{}*_bold.*".format(label, label)
+                            "sub-{}/ses-*/func/sub-{}*_bold.*".format(label, label)
                         )
             else:
                 for label in self.list_of_subjects_to_be_processed:
                     datalad_get_list.append(
-                            "sub-{}/anat/sub-{}*_T1w.*".format(label, label)
+                        "sub-{}/anat/sub-{}*_T1w.*".format(label, label)
                     )
                     datalad_get_list.append(
-                            "derivatives/{}/sub-{}/*".format(__freesurfer_directory__, label)
+                        "derivatives/{}/sub-{}/*".format(__freesurfer_directory__, label)
                     )
                     if self.run_dmri_pipeline:
                         datalad_get_list.append(
-                                "sub-{}/dwi/sub-{}*_dwi.*".format(label, label)
+                            "sub-{}/dwi/sub-{}*_dwi.*".format(label, label)
                         )
                     if self.run_fmri_pipeline:
                         datalad_get_list.append(
-                                "sub-{}/func/sub-{}*_bold.*".format(label, label)
+                            "sub-{}/func/sub-{}*_bold.*".format(label, label)
                         )
 
             cmd = (
-                    'datalad save -d . -m "Dataset state after adding the container image. '
-                    'Datasets ready to get files via datalad run."'
+                'datalad save -d . -m "Dataset state after adding the container image. '
+                'Datasets ready to get files via datalad run."'
             )
             try:
                 print_blue(f"... cmd: {cmd}")
                 self.run(cmd, env={}, cwd=os.path.abspath(self.bids_root))
             except Exception:
-                print_error(
-                        "    DATALAD ERROR: Failed to add existing files to dataset"
-                )
+                print_error("    DATALAD ERROR: Failed to add existing files to dataset")
 
             cmd = 'datalad run -d . -m "Get files for sub-{}" bash -c "datalad get {}"'.format(
-                    self.list_of_subjects_to_be_processed, " ".join(datalad_get_list)
+                self.list_of_subjects_to_be_processed, " ".join(datalad_get_list)
             )
             try:
                 print_blue(f"... cmd: {cmd}")
                 self.run(cmd, env={}, cwd=os.path.abspath(self.bids_root))
             except Exception:
                 print_error(
-                        "    DATALAD ERROR: Failed to get files (cmd: datalad get {})".format(
-                                " ".join(datalad_get_list)
-                        )
+                    "    DATALAD ERROR: Failed to get files (cmd: datalad get {})".format(
+                        " ".join(datalad_get_list)
+                    )
                 )
 
             cmd = (
-                    'datalad save -d . -m "Dataset state after getting the files. Dataset ready for connectome mapping." '
-                    "--version-tag ready4analysis-{}".format(time.strftime("%Y%m%d-%H%M%S"))
+                'datalad save -d . -m "Dataset state after getting the files. Dataset ready for connectome mapping." '
+                "--version-tag ready4analysis-{}".format(time.strftime("%Y%m%d-%H%M%S"))
             )
             try:
                 print_blue(f"... cmd: {cmd}")
@@ -1232,6 +1194,11 @@ def start_bids_app(self):
             except Exception:
                 print_error("    DATALAD ERROR: Failed to run datalad rev-status")
 
+        # Create and start the carbon footprint tracker
+        if self.track_carbon_footprint:
+            tracker = create_emissions_tracker(bids_root=self.bids_root)
+            tracker.start()
+
         # maxprocs = multiprocessing.cpu_count()
         processes = []
 
@@ -1240,12 +1207,12 @@ def start_bids_app(self):
         if self.datalad_is_available and self.data_provenance_tracking:
 
             proc = self.start_bidsapp_participant_level_process_with_datalad(
-                    self.bidsapp_tag, self.list_of_subjects_to_be_processed
+                self.bidsapp_tag, self.list_of_subjects_to_be_processed
             )
 
         else:
             proc = self.start_bidsapp_participant_level_process(
-                    self.bidsapp_tag, self.list_of_subjects_to_be_processed
+                self.bidsapp_tag, self.list_of_subjects_to_be_processed
             )
 
         processes.append(proc)
@@ -1258,14 +1225,14 @@ def start_bids_app(self):
             # project.clean_cache(self.bids_root)
 
             cmd = 'datalad save -d . -m "Dataset processed by the connectomemapper-bidsapp:{}" --version-tag processed-{}'.format(
-                    self.bidsapp_tag, time.strftime("%Y%m%d-%H%M%S")
+                self.bidsapp_tag, time.strftime("%Y%m%d-%H%M%S")
             )
             try:
                 print_blue(f"... cmd: {cmd}")
                 self.run(cmd, env={}, cwd=os.path.abspath(self.bids_root))
             except Exception:
                 print_error(
-                        "    DATALAD ERROR: Failed to commit derivatives to datalad dataset"
+                    "    DATALAD ERROR: Failed to commit derivatives to datalad dataset"
                 )
 
             cmd = "datalad diff -t HEAD~1"
@@ -1275,8 +1242,26 @@ def start_bids_app(self):
             except Exception:
                 print_error("    DATALAD ERROR: Failed to run datalad diff -t HEAD~1")
 
-        print("Processing with BIDS App Finished")
+        print("Processing with BIDS App Finished\n")
         self.docker_running = False
+
+        if self.track_carbon_footprint:
+            # Stop the carbon tracker
+            tracker.stop()
+            # Output the carbon footprint message to the terminal
+            carbonfootprint_msg = create_carbon_footprint_message(
+                bids_dir=self.bids_root,
+                emissions_csv_file=str(Path(self.bids_root) / 'code' / 'emissions.csv'),
+                nb_of_subjects_processed=len(self.list_of_subjects_to_be_processed)
+            )
+            print(carbonfootprint_msg)
+            # Display the carbon footprint report in a Dialog Window
+            self.carbon_emission_msg = create_html_carbon_footprint_report(
+                emissions_csv_file=str(Path(self.bids_root) / "code" / "emissions.csv"),
+                nb_of_subjects_processed=len(self.list_of_subjects_to_be_processed)
+            )
+            self.configure_traits(view='carbon_footprint_view')
+
         return True
 
     # def stop_bids_app(self, ui_info):
diff --git a/cmp/bidsappmanager/gui/handlers.py b/cmp/bidsappmanager/gui/handlers.py
index ba8f9a9db..0e46a8ed7 100644
--- a/cmp/bidsappmanager/gui/handlers.py
+++ b/cmp/bidsappmanager/gui/handlers.py
@@ -1542,7 +1542,7 @@ def load_dataset(self, ui_info, debug=False):
                             subject=subject,
                             session=sessions[0],
                             suffix="bold",
-                            extensions=["nii", "nii.gz"],
+                            extension=["nii", "nii.gz"],
                         )
                     ]
                     if len(query_files) > 0:
@@ -1555,7 +1555,7 @@ def load_dataset(self, ui_info, debug=False):
                             subject=subject,
                             session=sessions[0],
                             suffix="T1w",
-                            extensions=["nii", "nii.gz"],
+                            extension=["nii", "nii.gz"],
                         )
                     ]
                     if len(query_files) > 0:
@@ -1568,7 +1568,7 @@ def load_dataset(self, ui_info, debug=False):
                             subject=subject,
                             session=sessions[0],
                             suffix="T2w",
-                            extensions=["nii", "nii.gz"],
+                            extension=["nii", "nii.gz"],
                         )
                     ]
                     if len(query_files) > 0:
@@ -1581,7 +1581,7 @@ def load_dataset(self, ui_info, debug=False):
                             subject=subject,
                             session=sessions[0],
                             suffix="dwi",
-                            extensions=["nii", "nii.gz"],
+                            extension=["nii", "nii.gz"],
                         )
                     ]
                     if len(query_files) > 0:
@@ -1595,7 +1595,7 @@ def load_dataset(self, ui_info, debug=False):
                     query_files = [
                         f.filename
                         for f in bids_layout.get(
-                            subject=subject, suffix="T1w", extensions=["nii", "nii.gz"]
+                            subject=subject, suffix="T1w", extension=["nii", "nii.gz"]
                         )
                     ]
                     if len(query_files) > 0:
@@ -1605,7 +1605,7 @@ def load_dataset(self, ui_info, debug=False):
                     query_files = [
                         f.filename
                         for f in bids_layout.get(
-                            subject=subject, suffix="T2w", extensions=["nii", "nii.gz"]
+                            subject=subject, suffix="T2w", extension=["nii", "nii.gz"]
                         )
                     ]
                     if len(query_files) > 0:
@@ -1615,7 +1615,7 @@ def load_dataset(self, ui_info, debug=False):
                     query_files = [
                         f.filename
                         for f in bids_layout.get(
-                            subject=subject, suffix="dwi", extensions=["nii", "nii.gz"]
+                            subject=subject, suffix="dwi", extension=["nii", "nii.gz"]
                         )
                     ]
                     if len(query_files) > 0:
@@ -1625,7 +1625,7 @@ def load_dataset(self, ui_info, debug=False):
                     query_files = [
                         f.filename
                         for f in bids_layout.get(
-                            subject=subject, suffix="bold", extensions=["nii", "nii.gz"]
+                            subject=subject, suffix="bold", extension=["nii", "nii.gz"]
                         )
                     ]
                     if len(query_files) > 0:
@@ -1783,7 +1783,7 @@ def load_dataset(self, ui_info, debug=False):
                                     suffix="dwi",
                                     target="acquisition",
                                     return_type="id",
-                                    extensions=["nii", "nii.gz"],
+                                    extension=["nii", "nii.gz"],
                                 )
                             ]
                             if debug:
@@ -1842,7 +1842,7 @@ def load_dataset(self, ui_info, debug=False):
                                     subject=subject,
                                     session=session,
                                     suffix="dwi",
-                                    extensions=["nii", "nii.gz"],
+                                    extension=["nii", "nii.gz"],
                                 )
                             ]
 
@@ -1870,7 +1870,7 @@ def load_dataset(self, ui_info, debug=False):
                                     suffix="dwi",
                                     target="acquisition",
                                     return_type="id",
-                                    extensions=["nii", "nii.gz"],
+                                    extension=["nii", "nii.gz"],
                                 )
                             ]
 
@@ -2244,4 +2244,4 @@ def stop_bids_app(ui_info):
         print("Stop BIDS App")
         # self.docker_process.kill()
         ui_info.ui.context["object"].docker_running = False
-        return True
\ No newline at end of file
+        return True
diff --git a/cmp/bidsappmanager/gui/principal.py b/cmp/bidsappmanager/gui/principal.py
index 0e18d2309..f4bdd09b2 100644
--- a/cmp/bidsappmanager/gui/principal.py
+++ b/cmp/bidsappmanager/gui/principal.py
@@ -216,8 +216,8 @@ def _bidsapp_fired(self):
         self.bidsapp_ui = cmp.bidsappmanager.gui.bidsapp.BIDSAppInterfaceWindow(
             project_info=self.project_info,
             bids_root=self.project_info.base_directory,
-            subjects=subjects,
-            list_of_subjects_to_be_processed=subjects,
+            subjects=sorted(subjects),
+            list_of_subjects_to_be_processed=sorted(subjects),
             # anat_config=self.project_info.anat_config_file,
             # dmri_config=self.project_info.dmri_config_file,
             # fmri_config=self.project_info.fmri_config_file
diff --git a/cmp/bidsappmanager/pipelines/anatomical/anatomical.py b/cmp/bidsappmanager/pipelines/anatomical/anatomical.py
index 16a5dcf83..d3746252d 100644
--- a/cmp/bidsappmanager/pipelines/anatomical/anatomical.py
+++ b/cmp/bidsappmanager/pipelines/anatomical/anatomical.py
@@ -251,7 +251,7 @@ def check_input(self, layout):
             subject=subjid,
             session=None if (self.global_conf.subject_session == "") else sessid,
             suffix="T1w",
-            extension=".nii.gz",
+            extension="nii.gz",
         )
         if len(files) > 0:
             T1_file = files[0].filename
@@ -343,7 +343,7 @@ def check_input(self, layout):
                 suffix=self.stages["Parcellation"].config.custom_parcellation.suffix,
                 atlas=self.stages["Parcellation"].config.custom_parcellation.atlas,
                 resolution=self.stages["Parcellation"].config.custom_parcellation.resolution,
-                extension=".nii.gz",
+                extension="nii.gz",
             )
             if len(files) > 0:
                 custom_parc_file = os.path.join(files[0].dirname, files[0].filename)
@@ -358,7 +358,7 @@ def check_input(self, layout):
                          if self.global_conf.subject_session == ""
                          else self.global_conf.subject_session.split("-")[1]),
                 suffix=self.stages["Parcellation"].config.custom_parcellation.suffix,
-                extension=".tsv",
+                extension="tsv",
                 atlas=self.stages["Parcellation"].config.custom_parcellation.atlas,
                 resolution=self.stages["Parcellation"].config.custom_parcellation.resolution,
             )
@@ -379,7 +379,7 @@ def check_input(self, layout):
                              if self.global_conf.subject_session == ""
                              else self.global_conf.subject_session.split("-")[1]),
                     suffix=self.stages["Segmentation"].config.custom_brainmask.suffix,
-                    extension=".nii.gz",
+                    extension="nii.gz",
                     desc=self.stages["Segmentation"].config.custom_brainmask.desc,
             )
             if len(files) > 0:
@@ -399,7 +399,7 @@ def check_input(self, layout):
                          if self.global_conf.subject_session == ""
                          else self.global_conf.subject_session.split("-")[1]),
                 suffix=self.stages["Segmentation"].config.custom_gm_mask.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 label=self.stages["Segmentation"].config.custom_gm_mask.label,
             )
             if len(files) > 0:
@@ -419,7 +419,7 @@ def check_input(self, layout):
                          if self.global_conf.subject_session == ""
                          else self.global_conf.subject_session.split("-")[1]),
                 suffix=self.stages["Segmentation"].config.custom_wm_mask.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 label=self.stages["Segmentation"].config.custom_wm_mask.label,
             )
             if len(files) > 0:
@@ -439,7 +439,7 @@ def check_input(self, layout):
                          if self.global_conf.subject_session == ""
                          else self.global_conf.subject_session.split("-")[1]),
                 suffix=self.stages["Segmentation"].config.custom_csf_mask.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 label=self.stages["Segmentation"].config.custom_csf_mask.label,
             )
             if len(files) > 0:
@@ -459,7 +459,7 @@ def check_input(self, layout):
                          if self.global_conf.subject_session == ""
                          else self.global_conf.subject_session.split("-")[1]),
                 suffix=self.stages["Segmentation"].config.custom_aparcaseg.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 desc=self.stages["Segmentation"].config.custom_aparcaseg.desc,
             )
             if len(files) > 0:
diff --git a/cmp/bidsappmanager/pipelines/diffusion/diffusion.py b/cmp/bidsappmanager/pipelines/diffusion/diffusion.py
index b53016625..716706a84 100644
--- a/cmp/bidsappmanager/pipelines/diffusion/diffusion.py
+++ b/cmp/bidsappmanager/pipelines/diffusion/diffusion.py
@@ -313,7 +313,7 @@ def check_input(self, layout, gui=True):
 
             if self.global_conf.subject_session == "":
 
-                files = layout.get(subject=subjid, suffix="dwi", extensions=".nii.gz")
+                files = layout.get(subject=subjid, suffix="dwi", extension="nii.gz")
                 if len(files) > 0:
                     dwi_file = os.path.join(files[0].dirname, files[0].filename)
                     print(dwi_file)
@@ -326,7 +326,7 @@ def check_input(self, layout, gui=True):
                     )
                     return
 
-                files = layout.get(subject=subjid, suffix="dwi", extensions=".bval")
+                files = layout.get(subject=subjid, suffix="dwi", extension="bval")
                 if len(files) > 0:
                     bval_file = os.path.join(files[0].dirname, files[0].filename)
                     print(bval_file)
@@ -340,7 +340,7 @@ def check_input(self, layout, gui=True):
                     )
                     return
 
-                files = layout.get(subject=subjid, suffix="dwi", extensions=".bvec")
+                files = layout.get(subject=subjid, suffix="dwi", extension="bvec")
                 if len(files) > 0:
                     bvec_file = os.path.join(files[0].dirname, files[0].filename)
                     print(bvec_file)
@@ -357,7 +357,7 @@ def check_input(self, layout, gui=True):
                 sessid = self.global_conf.subject_session.split("-")[1]
 
                 files = layout.get(
-                    subject=subjid, suffix="dwi", extensions=".nii.gz", session=sessid
+                    subject=subjid, suffix="dwi", extension="nii.gz", session=sessid
                 )
                 if len(files) > 0:
                     dwi_file = os.path.join(files[0].dirname, files[0].filename)
@@ -373,7 +373,7 @@ def check_input(self, layout, gui=True):
                     return
 
                 files = layout.get(
-                    subject=subjid, suffix="dwi", extensions=".bval", session=sessid
+                    subject=subjid, suffix="dwi", extension="bval", session=sessid
                 )
                 if len(files) > 0:
                     bval_file = os.path.join(files[0].dirname, files[0].filename)
@@ -389,7 +389,7 @@ def check_input(self, layout, gui=True):
                     return
 
                 files = layout.get(
-                    subject=subjid, suffix="dwi", extensions=".bvec", session=sessid
+                    subject=subjid, suffix="dwi", extension="bvec", session=sessid
                 )
                 if len(files) > 0:
                     bvec_file = os.path.join(files[0].dirname, files[0].filename)
diff --git a/cmp/bidsappmanager/pipelines/functional/fMRI.py b/cmp/bidsappmanager/pipelines/functional/fMRI.py
index 0064e5c21..ccdc942da 100644
--- a/cmp/bidsappmanager/pipelines/functional/fMRI.py
+++ b/cmp/bidsappmanager/pipelines/functional/fMRI.py
@@ -297,7 +297,7 @@ def check_input(self, layout, gui=True):
 
         if self.global_conf.subject_session == "":
 
-            files = layout.get(subject=subjid, suffix="bold", extensions=".nii.gz")
+            files = layout.get(subject=subjid, suffix="bold", extension="nii.gz")
             if len(files) > 0:
                 fmri_file = os.path.join(files[0].dirname, files[0].filename)
                 print(fmri_file)
@@ -310,7 +310,7 @@ def check_input(self, layout, gui=True):
                 )
                 return
 
-            files = layout.get(subject=subjid, suffix="bold", extensions=".json")
+            files = layout.get(subject=subjid, suffix="bold", extension="json")
             if len(files) > 0:
                 json_file = os.path.join(files[0].dirname, files[0].filename)
                 print(json_file)
@@ -322,7 +322,7 @@ def check_input(self, layout, gui=True):
                     parent=None,
                 )
 
-            files = layout.get(subject=subjid, suffix="T1w", extensions=".nii.gz")
+            files = layout.get(subject=subjid, suffix="T1w", extension="nii.gz")
             if len(files) > 0:
                 t1_file = os.path.join(files[0].dirname, files[0].filename)
                 print(t1_file)
@@ -335,7 +335,7 @@ def check_input(self, layout, gui=True):
                 )
                 return
 
-            files = layout.get(subject=subjid, suffix="T2w", extensions=".nii.gz")
+            files = layout.get(subject=subjid, suffix="T2w", extension=".nii.gz")
             if len(files) > 0:
                 t2_file = os.path.join(files[0].dirname, files[0].filename)
                 print(t2_file)
@@ -351,7 +351,7 @@ def check_input(self, layout, gui=True):
             sessid = self.global_conf.subject_session.split("-")[1]
 
             files = layout.get(
-                subject=subjid, suffix="bold", extensions=".nii.gz", session=sessid
+                subject=subjid, suffix="bold", extension=".nii.gz", session=sessid
             )
             if len(files) > 0:
                 fmri_file = os.path.join(files[0].dirname, files[0].filename)
@@ -367,7 +367,7 @@ def check_input(self, layout, gui=True):
                 return
 
             files = layout.get(
-                subject=subjid, suffix="bold", extensions=".json", session=sessid
+                subject=subjid, suffix="bold", extension=".json", session=sessid
             )
             if len(files) > 0:
                 json_file = os.path.join(files[0].dirname, files[0].filename)
@@ -382,7 +382,7 @@ def check_input(self, layout, gui=True):
                 )
 
             files = layout.get(
-                subject=subjid, suffix="T1w", extensions=".nii.gz", session=sessid
+                subject=subjid, suffix="T1w", extension=".nii.gz", session=sessid
             )
             if len(files) > 0:
                 t1_file = os.path.join(files[0].dirname, files[0].filename)
@@ -398,7 +398,7 @@ def check_input(self, layout, gui=True):
                 return
 
             files = layout.get(
-                subject=subjid, suffix="T2w", extensions=".nii.gz", session=sessid
+                subject=subjid, suffix="T2w", extension=".nii.gz", session=sessid
             )
             if len(files) > 0:
                 t2_file = os.path.join(files[0].dirname, files[0].filename)
diff --git a/cmp/cli/connectomemapper3_docker.py b/cmp/cli/connectomemapper3_docker.py
index 741570b68..a1a29cf06 100644
--- a/cmp/cli/connectomemapper3_docker.py
+++ b/cmp/cli/connectomemapper3_docker.py
@@ -8,11 +8,16 @@
 
 # General imports
 import sys
+from pathlib import Path
 
 # Own imports
 from cmp.parser import get_docker_wrapper_parser
 from cmtklib.util import check_directory_exists
 from cmtklib.process import run
+from cmtklib.carbonfootprint import (
+    create_emissions_tracker,
+    create_carbon_footprint_message
+)
 
 
 def create_docker_cmd(args):
@@ -116,6 +121,11 @@ def main():
     # Create the docker run command
     cmd = create_docker_cmd(args)
 
+    if args.track_carbon_footprint:
+        # Create and start the carbon footprint tracker
+        tracker = create_emissions_tracker(bids_root=args.bids_dir)
+        tracker.start()
+
     # Execute the docker run command
     try:
         print(f'... cmd: {cmd}')
@@ -126,6 +136,17 @@ def main():
         print(e)
         exit_code = 1
 
+    if args.track_carbon_footprint:
+        # Stop the carbon tracker
+        tracker.stop()
+        # Output the carbon footprint message to the terminal
+        carbonfootprint_msg = create_carbon_footprint_message(
+            bids_dir=args.bids_dir,
+            emissions_csv_file=str(Path(args.bids_dir) / 'code' / 'emissions.csv'),
+            nb_of_subjects_processed=len(args.participant_label)
+        )
+        print(carbonfootprint_msg)
+
     return exit_code
 
 
diff --git a/cmp/cli/connectomemapper3_singularity.py b/cmp/cli/connectomemapper3_singularity.py
index 75412630b..218710b26 100644
--- a/cmp/cli/connectomemapper3_singularity.py
+++ b/cmp/cli/connectomemapper3_singularity.py
@@ -8,11 +8,16 @@
 
 # General imports
 import sys
+from pathlib import Path
 
 # Own imports
 from cmp.parser import get_singularity_wrapper_parser
 from cmtklib.util import check_directory_exists
 from cmtklib.process import run
+from cmtklib.carbonfootprint import (
+    create_emissions_tracker,
+    create_carbon_footprint_message
+)
 
 
 def create_singularity_cmd(args):
@@ -118,6 +123,11 @@ def main():
     # Create the singularity run command
     cmd = create_singularity_cmd(args)
 
+    if args.track_carbon_footprint:
+        # Create and start the carbon footprint tracker
+        tracker = create_emissions_tracker(bids_root=args.bids_dir)
+        tracker.start()
+
     # Execute the singularity run command
     try:
         print(f'... cmd: {cmd}')
@@ -128,6 +138,17 @@ def main():
         print(e)
         exit_code = 1
 
+    if args.track_carbon_footprint:
+        # Stop the carbon tracker
+        tracker.stop()
+        # Output the carbon footprint message to the terminal
+        carbonfootprint_msg = create_carbon_footprint_message(
+            bids_dir=args.bids_dir,
+            emissions_csv_file=str(Path(args.bids_dir) / 'code' / 'emissions.csv'),
+            nb_of_subjects_processed=len(args.participant_label)
+        )
+        print(carbonfootprint_msg)
+
     return exit_code
 
 
diff --git a/cmp/info.py b/cmp/info.py
index a81846489..5a9173095 100644
--- a/cmp/info.py
+++ b/cmp/info.py
@@ -7,9 +7,9 @@
 
 _version_major = 3
 _version_minor = 0
-_version_micro = 1
+_version_micro = 2
 _version_extra = ""
-__release_date__ = "05.01.2022"
+__release_date__ = "21.01.2022"
 
 __minor_version__ = "%s.%s" % (_version_major, _version_minor)
 
diff --git a/cmp/parser.py b/cmp/parser.py
index 6351ece4f..f5ffa6513 100644
--- a/cmp/parser.py
+++ b/cmp/parser.py
@@ -12,13 +12,13 @@
 from .info import __release_date__
 
 
-def get():
+def get() -> argparse.ArgumentParser:
     """Return the argparse parser of the BIDS App.
 
     Returns
     -------
-    p : object
-       Instance of :class:`argparse.ArgumentParser` class
+    p : argparse.ArgumentParser
+       Instance of :class:`argparse.ArgumentParser`
     """
 
     p = argparse.ArgumentParser(
@@ -141,16 +141,29 @@ def get():
     return p
 
 
-def get_docker_wrapper_parser():
+def get_wrapper_parser() -> argparse.ArgumentParser:
+    """Create and return the parser object of the python wrappers of the BIDS App."""
+    p: argparse.ArgumentParser = get()
+    p.add_argument(
+        '--track_carbon_footprint',
+        dest='track_carbon_footprint',
+        action='store_true',
+        help="Track carbon footprint with `codecarbon <https://codecarbon.io/>`_ and save results in "
+             "a CSV file called ``emissions.csv`` in the ``<bids_dir>/code`` directory.",
+    )
+    return p
+
+
+def get_docker_wrapper_parser() -> argparse.ArgumentParser:
     """Return the argparse parser of the Docker BIDS App.
     
     Returns
     -------
-    p : object
-       Instance of :class:`argparse.ArgumentParser` class
+    p : argparse.ArgumentParser
+       Instance of :class:`argparse.ArgumentParser`
     """
-    p = get()
-    p.description = f"Entrypoint script of the BIDS-App Connectome Mapper version {__version__} via Docker."
+    p: argparse.ArgumentParser = get_wrapper_parser()
+    p.description = f"Entrypoint script of the Connectome Mapper BIDS-App version {__version__} via Docker."
     p.add_argument(
         '--docker_image',
         type=str,
@@ -166,16 +179,16 @@ def get_docker_wrapper_parser():
     return p
 
 
-def get_singularity_wrapper_parser():
+def get_singularity_wrapper_parser() -> argparse.ArgumentParser:
     """Return the argparse parser of the Singularity BIDS App.
     
     Returns
     -------
-    p : object
-       Instance of :class:`argparse.ArgumentParser` class
+    p : argparse.ArgumentParser
+       Instance of :class:`argparse.ArgumentParser`
     """
-    p = get()
-    p.description = f"Entrypoint script of the BIDS-App Connectome Mapper version {__version__} via Singularity."
+    p: argparse.ArgumentParser = get_wrapper_parser()
+    p.description = f"Entrypoint script of the Connectome Mapper BIDS-App version {__version__} via Singularity."
     p.add_argument(
         '--singularity_image',
         type=str,
diff --git a/cmp/pipelines/anatomical/anatomical.py b/cmp/pipelines/anatomical/anatomical.py
index 4b8237c67..4f5e790a8 100644
--- a/cmp/pipelines/anatomical/anatomical.py
+++ b/cmp/pipelines/anatomical/anatomical.py
@@ -246,7 +246,7 @@ def check_input(self, layout, gui=True):
         subjid = self.subject.split("-")[1]
 
         if self.global_conf.subject_session == "":
-            files = layout.get(subject=subjid, suffix="T1w", extension=".nii.gz")
+            files = layout.get(subject=subjid, suffix="T1w", extension="nii.gz")
             if len(files) > 0:
                 T1_file = os.path.join(files[0].dirname, files[0].filename)
                 print(T1_file)
@@ -255,7 +255,7 @@ def check_input(self, layout, gui=True):
         else:
             sessid = self.global_conf.subject_session.split("-")[1]
             files = layout.get(
-                subject=subjid, suffix="T1w", extension=".nii.gz", session=sessid
+                subject=subjid, suffix="T1w", extension="nii.gz", session=sessid
             )
             if len(files) > 0:
                 T1_file = os.path.join(files[0].dirname, files[0].filename)
@@ -266,7 +266,7 @@ def check_input(self, layout, gui=True):
         print("... t1_file : %s" % T1_file)
 
         if self.global_conf.subject_session == "":
-            files = layout.get(subject=subjid, suffix="T1w", extension=".json")
+            files = layout.get(subject=subjid, suffix="T1w", extension="json")
             if len(files) > 0:
                 T1_json_file = os.path.join(files[0].dirname, files[0].filename)
                 print(T1_json_file)
@@ -275,7 +275,7 @@ def check_input(self, layout, gui=True):
         else:
             sessid = self.global_conf.subject_session.split("-")[1]
             files = layout.get(
-                subject=subjid, suffix="T1w", extension=".json", session=sessid
+                subject=subjid, suffix="T1w", extension="json", session=sessid
             )
             if len(files) > 0:
                 T1_json_file = os.path.join(files[0].dirname, files[0].filename)
@@ -413,7 +413,7 @@ def check_input(self, layout, gui=True):
                          if self.global_conf.subject_session != ""
                          else None),
                 suffix=self.stages["Parcellation"].config.custom_parcellation.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 atlas=self.stages["Parcellation"].config.custom_parcellation.atlas,
                 res=self.stages["Parcellation"].config.custom_parcellation.res,
             )
@@ -430,7 +430,7 @@ def check_input(self, layout, gui=True):
                          if self.global_conf.subject_session != ""
                          else None),
                 suffix=self.stages["Parcellation"].config.custom_parcellation.suffix,
-                extension=".tsv",
+                extension="tsv",
                 atlas=self.stages["Parcellation"].config.custom_parcellation.atlas,
                 res=self.stages["Parcellation"].config.custom_parcellation.res,
             )
@@ -450,7 +450,7 @@ def check_input(self, layout, gui=True):
                              if self.global_conf.subject_session != ""
                              else None),
                     suffix=self.stages["Segmentation"].config.custom_brainmask.suffix,
-                    extension=".nii.gz",
+                    extension="nii.gz",
                     desc=self.stages["Segmentation"].config.custom_brainmask.desc,
             )
             if len(files) > 0:
@@ -469,7 +469,7 @@ def check_input(self, layout, gui=True):
                          if self.global_conf.subject_session != ""
                          else None),
                 suffix=self.stages["Segmentation"].config.custom_gm_mask.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 label=self.stages["Segmentation"].config.custom_gm_mask.label,
             )
             if len(files) > 0:
@@ -488,7 +488,7 @@ def check_input(self, layout, gui=True):
                          if self.global_conf.subject_session != ""
                          else None),
                 suffix=self.stages["Segmentation"].config.custom_wm_mask.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 label=self.stages["Segmentation"].config.custom_wm_mask.label,
             )
             if len(files) > 0:
@@ -507,7 +507,7 @@ def check_input(self, layout, gui=True):
                          if self.global_conf.subject_session != ""
                          else None),
                 suffix=self.stages["Segmentation"].config.custom_csf_mask.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 label=self.stages["Segmentation"].config.custom_csf_mask.label,
             )
             if len(files) > 0:
@@ -526,7 +526,7 @@ def check_input(self, layout, gui=True):
                          if self.global_conf.subject_session != ""
                          else None),
                 suffix=self.stages["Segmentation"].config.custom_aparcaseg.suffix,
-                extension=".nii.gz",
+                extension="nii.gz",
                 desc=self.stages["Segmentation"].config.custom_aparcaseg.desc,
             )
             if len(files) > 0:
@@ -897,7 +897,19 @@ def create_pipeline_flow(
         )
         # fmt:on
 
+        self.stages[
+            "Segmentation"
+        ].config.freesurfer_subjects_dir = os.path.join(
+            self.output_directory, __freesurfer_directory__
+        )
+        self.stages[
+            "Segmentation"
+        ].config.freesurfer_subject_id = os.path.join(
+            self.output_directory, __freesurfer_directory__, self.subject
+        )
+
         seg_flow = self.create_stage_flow("Segmentation")
+
         # fmt: off
         anat_flow.connect(
             [
@@ -910,17 +922,6 @@ def create_pipeline_flow(
 
         if self.stages["Segmentation"].config.seg_tool == "Freesurfer":
 
-            self.stages[
-                "Segmentation"
-            ].config.freesurfer_subjects_dir = os.path.join(
-                self.output_directory, __freesurfer_directory__
-            )
-            self.stages[
-                "Segmentation"
-            ].config.freesurfer_subject_id = os.path.join(
-                self.output_directory, __freesurfer_directory__, self.subject
-            )
-
             # fmt: off
             anat_flow.connect(
                 [
@@ -1001,14 +1002,14 @@ def create_pipeline_flow(
         self.flow = anat_flow
         return anat_flow
 
-    def process(self):
-        """Executes the anatomical pipeline workflow and returns True if successful."""
-        # Enable the use of the W3C PROV data model to capture and represent provenance in Nipype
-        # config.enable_provenance()
-
-        # Process time
-        self.now = datetime.datetime.now().strftime("%Y%m%d_%H%M")
+    def init_subject_derivatives_dirs(self):
+        """Return the paths to Nipype and CMP derivatives folders of a given subject / session.
 
+        Notes
+        -----
+        `self.subject` is updated to "sub-<participant_label>_ses-<session_label>"
+        when subject has multiple sessions.
+        """
         if "_" in self.subject:
             self.subject = self.subject.split("_")[0]
 
@@ -1042,6 +1043,25 @@ def process(self):
             except os.error:
                 print("%s was already existing" % nipype_anatomical_pipeline_subject_dir)
 
+        return cmp_deriv_subject_directory, nipype_deriv_subject_directory, nipype_anatomical_pipeline_subject_dir
+
+    def process(self):
+        """Executes the anatomical pipeline workflow and returns True if successful."""
+        anat_flow = None  # noqa
+
+        # Enable the use of the W3C PROV data model to capture and represent provenance in Nipype
+        # config.enable_provenance()
+
+        # Process time
+        self.now = datetime.datetime.now().strftime("%Y%m%d_%H%M")
+
+        # Create the paths <output_dir>/cmp-<version>/sub-<label>(/ses-<label>)
+        # and <output_dir>/nipype-<version>/sub-<label>(/ses-<label>)
+        # self.subject is updated to "sub-<label>_ses-<label>"
+        # when subject has multiple sessions.
+        cmp_deriv_subject_directory, nipype_deriv_subject_directory, nipype_anatomical_pipeline_subject_dir = \
+            self.init_subject_derivatives_dirs()
+
         # Initialization
         if os.path.isfile(os.path.join(nipype_anatomical_pipeline_subject_dir, "pypeline.log")):
             os.unlink(os.path.join(nipype_anatomical_pipeline_subject_dir, "pypeline.log"))
@@ -1049,8 +1069,8 @@ def process(self):
         config.update_config(
             {
                 "logging": {
-                    "workflow_level": "DEBUG",
-                    "interface_level": "DEBUG",
+                    "workflow_level": "INFO",
+                    "interface_level": "INFO",
                     "log_directory": os.path.join(
                         nipype_deriv_subject_directory, "anatomical_pipeline"
                     ),
@@ -1077,12 +1097,9 @@ def process(self):
         )
         anat_flow.write_graph(graph2use="colored", format="svg", simple_form=True)
 
-        if self.number_of_cores != 1:
-            anat_flow.run(
-                plugin="MultiProc", plugin_args={"n_procs": self.number_of_cores}
-            )
-        else:
-            anat_flow.run()
+        anat_flow.run(
+            plugin="MultiProc", plugin_args={"n_procs": self.number_of_cores}
+        )
 
         self._update_parcellation_scheme()
 
diff --git a/cmp/pipelines/diffusion/diffusion.py b/cmp/pipelines/diffusion/diffusion.py
index 68c85bb53..4d57b61ba 100644
--- a/cmp/pipelines/diffusion/diffusion.py
+++ b/cmp/pipelines/diffusion/diffusion.py
@@ -320,7 +320,7 @@ def define_custom_mapping(self, custom_last_stage):
     def _atlas_info_changed(self, new):
         pass
 
-    def get_file(self, layout, subject, suffix, extensions, session=None):
+    def get_file(self, layout, subject, suffix, extension, session=None):
         """Query files with PyBIDS and take the first file in the returned list or get a specific dmri file if BIDS acq- keyword is used in filename.
 
         Parameters
@@ -334,7 +334,7 @@ def get_file(self, layout, subject, suffix, extensions, session=None):
         suffix : str
             BIDS file suffix i.e. "T1w", "dwi", ...
 
-        extensions : str
+        extension : str
             File extension i.e. ".nii.gz", ".json", ".bval", ...
 
         session : str
@@ -346,9 +346,9 @@ def get_file(self, layout, subject, suffix, extensions, session=None):
             The output filepath or None if no file was found
         """
         if session is None:
-            files = layout.get(subject=subject, suffix=suffix, extension=extensions)
+            files = layout.get(subject=subject, suffix=suffix, extension=extension)
         else:
-            files = layout.get(subject=subject, suffix=suffix, extension=extensions, session=session)
+            files = layout.get(subject=subject, suffix=suffix, extension=extension, session=session)
 
         if len(files) > 0:
             out_file = os.path.join(files[0].dirname, files[0].filename)
@@ -406,12 +406,12 @@ def check_input(self, layout, gui=True):
 
             if self.global_conf.subject_session == "":
 
-                dwi_file = self.get_file(layout, subject=subjid, suffix="dwi", extensions=".nii.gz")
+                dwi_file = self.get_file(layout, subject=subjid, suffix="dwi", extension="nii.gz")
                 if dwi_file is None:
                     print("ERROR : Diffusion image not found for subject %s." % subjid)
                     return
 
-                json_file = self.get_file(layout, subject=subjid, suffix="dwi", extensions=".json")
+                json_file = self.get_file(layout, subject=subjid, suffix="dwi", extension="json")
                 if json_file is None:
                     json_file = "NotFound"
                     print(
@@ -419,7 +419,7 @@ def check_input(self, layout, gui=True):
                         % subjid
                     )
 
-                bval_file = self.get_file(layout, subject=subjid, suffix="dwi", extensions=".bval")
+                bval_file = self.get_file(layout, subject=subjid, suffix="dwi", extension="bval")
                 if bval_file is None:
                     print(
                         "ERROR : Diffusion bval image not found for subject %s."
@@ -427,7 +427,7 @@ def check_input(self, layout, gui=True):
                     )
                     return
 
-                bvec_file = self.get_file(layout, subject=subjid, suffix="dwi", extensions=".bvec")
+                bvec_file = self.get_file(layout, subject=subjid, suffix="dwi", extension="bvec")
                 if bvec_file is None:
                     print(
                         "ERROR : Diffusion bvec image not found for subject %s."
@@ -437,7 +437,7 @@ def check_input(self, layout, gui=True):
             else:
                 sessid = self.global_conf.subject_session.split("-")[1]
 
-                dwi_file = self.get_file(layout, subject=subjid, suffix="dwi", extensions=".nii.gz", session=sessid)
+                dwi_file = self.get_file(layout, subject=subjid, suffix="dwi", extension="nii.gz", session=sessid)
                 if dwi_file is None:
                     print(
                         "ERROR : Diffusion image not found for subject %s, session %s."
@@ -446,7 +446,7 @@ def check_input(self, layout, gui=True):
                     return
 
                 json_file = self.get_file(
-                    layout, subject=subjid, suffix="dwi", extensions=".json", session=sessid
+                    layout, subject=subjid, suffix="dwi", extension="json", session=sessid
                 )
                 if json_file is None:
                     json_file = "NotFound"
@@ -456,7 +456,7 @@ def check_input(self, layout, gui=True):
                     )
 
                 bval_file = self.get_file(
-                    layout, subject=subjid, suffix="dwi", extensions=".bval", session=sessid
+                    layout, subject=subjid, suffix="dwi", extension="bval", session=sessid
                 )
                 if bval_file is None:
                     print(
@@ -466,7 +466,7 @@ def check_input(self, layout, gui=True):
                     return
 
                 bvec_file = self.get_file(
-                    layout, subject=subjid, suffix="dwi", extensions=".bvec", session=sessid
+                    layout, subject=subjid, suffix="dwi", extension="bvec", session=sessid
                 )
                 if bvec_file is None:
                     print(
diff --git a/cmp/pipelines/functional/fMRI.py b/cmp/pipelines/functional/fMRI.py
index 51470563f..36d1da07e 100644
--- a/cmp/pipelines/functional/fMRI.py
+++ b/cmp/pipelines/functional/fMRI.py
@@ -272,26 +272,26 @@ def check_input(self, layout, gui=True):
         print("> Looking for....")
         if self.global_conf.subject_session == "":
 
-            files = layout.get(subject=subjid, suffix="bold", extension=".nii.gz")
+            files = layout.get(subject=subjid, suffix="bold", extension="nii.gz")
             if len(files) > 0:
                 fmri_file = os.path.join(files[0].dirname, files[0].filename)
             else:
                 print("ERROR : BOLD image not found for subject %s." % subjid)
                 return
 
-            files = layout.get(subject=subjid, suffix="bold", extension=".json")
+            files = layout.get(subject=subjid, suffix="bold", extension="json")
             if len(files) > 0:
                 json_file = os.path.join(files[0].dirname, files[0].filename)
             else:
                 print("WARNING : BOLD json sidecar not found for subject %s." % subjid)
 
-            files = layout.get(subject=subjid, suffix="T1w", extension=".nii.gz")
+            files = layout.get(subject=subjid, suffix="T1w", extension="nii.gz")
             if len(files) > 0:
                 t1_file = os.path.join(files[0].dirname, files[0].filename)
             else:
                 print("WARNING : T1w image not found for subject %s." % subjid)
 
-            files = layout.get(subject=subjid, suffix="T2w", extension=".nii.gz")
+            files = layout.get(subject=subjid, suffix="T2w", extension="nii.gz")
             if len(files) > 0:
                 t2_file = os.path.join(files[0].dirname, files[0].filename)
             else:
@@ -301,7 +301,7 @@ def check_input(self, layout, gui=True):
             sessid = self.global_conf.subject_session.split("-")[1]
 
             files = layout.get(
-                subject=subjid, suffix="bold", extension=".nii.gz", session=sessid
+                subject=subjid, suffix="bold", extension="nii.gz", session=sessid
             )
             if len(files) > 0:
                 fmri_file = os.path.join(files[0].dirname, files[0].filename)
@@ -313,7 +313,7 @@ def check_input(self, layout, gui=True):
                 return
 
             files = layout.get(
-                subject=subjid, suffix="bold", extension=".json", session=sessid
+                subject=subjid, suffix="bold", extension="json", session=sessid
             )
             if len(files) > 0:
                 json_file = os.path.join(files[0].dirname, files[0].filename)
@@ -324,7 +324,7 @@ def check_input(self, layout, gui=True):
                 )
 
             files = layout.get(
-                subject=subjid, suffix="T1w", extension=".nii.gz", session=sessid
+                subject=subjid, suffix="T1w", extension="nii.gz", session=sessid
             )
             if len(files) > 0:
                 t1_file = os.path.join(files[0].dirname, files[0].filename)
@@ -335,7 +335,7 @@ def check_input(self, layout, gui=True):
                 )
 
             files = layout.get(
-                subject=subjid, suffix="T2w", extension=".nii.gz", session=sessid
+                subject=subjid, suffix="T2w", extension="nii.gz", session=sessid
             )
             if len(files) > 0:
                 t2_file = os.path.join(files[0].dirname, files[0].filename)
diff --git a/cmp/stages/diffusion/diffusion.py b/cmp/stages/diffusion/diffusion.py
index 401fd5b8f..7fb36f2a9 100644
--- a/cmp/stages/diffusion/diffusion.py
+++ b/cmp/stages/diffusion/diffusion.py
@@ -382,7 +382,10 @@ def create_workflow(self, flow, inputnode, outputnode):
         if self.config.dilate_rois:
 
             dilate_rois = pe.MapNode(
-                interface=fsl.DilateImage(), iterfield=["in_file"], name="dilate_rois"
+                interface=fsl.DilateImage(),
+                iterfield=["in_file"],
+                synchronize=True,
+                name="dilate_rois"
             )
             dilate_rois.inputs.operation = "modal"
 
diff --git a/cmp/stages/parcellation/parcellation.py b/cmp/stages/parcellation/parcellation.py
index 6064567af..9723e5054 100644
--- a/cmp/stages/parcellation/parcellation.py
+++ b/cmp/stages/parcellation/parcellation.py
@@ -314,8 +314,9 @@ def create_workflow(self, flow, inputnode, outputnode):
                 # fmt: on
                 createBIDSLabelIndexMappingFile = pe.MapNode(
                     interface=CreateBIDSStandardParcellationLabelIndexMappingFile(),
-                    name="createBIDSLabelIndexMappingFile",
-                    iterfield=['roi_graphml', 'roi_colorlut']
+                    iterfield=['roi_graphml', 'roi_colorlut'],
+                    synchronize=True,
+                    name="createBIDSLabelIndexMappingFile"
                 )
                 createBIDSLabelIndexMappingFile.inputs.verbose = True
                 # fmt: off
@@ -377,9 +378,10 @@ def create_workflow(self, flow, inputnode, outputnode):
                 )
                 # fmt: on
                 createBIDSLabelIndexMappingFile = pe.MapNode(
-                        interface=CreateBIDSStandardParcellationLabelIndexMappingFile(),
-                        name="createBIDSLabelIndexMappingFile",
-                        iterfield=['roi_graphml', 'roi_colorlut']
+                    interface=CreateBIDSStandardParcellationLabelIndexMappingFile(),
+                    iterfield=['roi_graphml', 'roi_colorlut'],
+                    synchronize=True,
+                    name="createBIDSLabelIndexMappingFile"
                 )
                 createBIDSLabelIndexMappingFile.inputs.verbose = True
                 # fmt: off
diff --git a/cmp/stages/preprocessing/preprocessing.py b/cmp/stages/preprocessing/preprocessing.py
index e3c827a16..3ddf68421 100644
--- a/cmp/stages/preprocessing/preprocessing.py
+++ b/cmp/stages/preprocessing/preprocessing.py
@@ -761,7 +761,8 @@ def create_workflow(self, flow, inputnode, outputnode):
         fs_mriconvert_ROIs = pe.MapNode(
             interface=fs.MRIConvert(out_type="niigz", resample_type="nearest"),
             iterfield=["in_file"],
-            name="ROIs_resample",
+            synchronize=True,
+            name="ROIs_resample"
         )
         fs_mriconvert_ROIs.inputs.vox_size = self.config.resampling
         # fmt: off
@@ -1033,7 +1034,8 @@ def create_workflow(self, flow, inputnode, outputnode):
                 fs_mriconvert_PVEs = pe.MapNode(
                     interface=fs.MRIConvert(out_type="niigz"),
                     iterfield=["in_file"],
-                    name="PVEs_resample",
+                    synchronize=True,
+                    name="PVEs_resample"
                 )
                 fs_mriconvert_PVEs.inputs.vox_size = self.config.resampling
                 fs_mriconvert_PVEs.inputs.resample_type = self.config.interpolation
diff --git a/cmp/stages/segmentation/segmentation.py b/cmp/stages/segmentation/segmentation.py
index c6272d77a..c87d79fc5 100644
--- a/cmp/stages/segmentation/segmentation.py
+++ b/cmp/stages/segmentation/segmentation.py
@@ -268,13 +268,13 @@ def create_workflow(self, flow, inputnode, outputnode):
         if self.config.seg_tool == "Freesurfer":
 
             def correct_freesurfer_subjectid_path(path):
-                if '/output_dir' not in path:
+                if os.path.exists('/output_dir') and '/output_dir' not in path:
                     subject_id = path.split(f"{__freesurfer_directory__}/")[-1]
                     path = os.path.abspath(f'/output_dir/{__freesurfer_directory__}/{subject_id}')
                 return path
 
             def correct_freesurfer_subjects_path(path):
-                if '/output_dir' not in path:
+                if os.path.exists('/output_dir') and '/output_dir' not in path:
                     path = os.path.abspath(f'/output_dir/{__freesurfer_directory__}')
                 return path
 
diff --git a/cmtklib/bids/io.py b/cmtklib/bids/io.py
index e5f57f4ee..d4c66490a 100644
--- a/cmtklib/bids/io.py
+++ b/cmtklib/bids/io.py
@@ -158,7 +158,7 @@ class CustomParcellationBIDSFile(CustomBIDSFile):
     """Represent a custom parcellation files in the form `sub-<label>_atlas-<label>[_res-<label>]_dseg.nii.gz`."""
 
     def __init__(self):
-        super().__init__(p_suffix="dseg", p_atlas="L2018", p_extension=".nii.gz")
+        super().__init__(p_suffix="dseg", p_atlas="L2018", p_extension="nii.gz")
 
     def get_nb_of_regions(self, bids_dir, subject, session=None, debug=True):
         """Return the number of regions by reading its associated TSV side car file describing the nodes.
@@ -203,32 +203,32 @@ class CustomBrainMaskBIDSFile(CustomBIDSFile):
     """Represent a custom brain mask in the form `sub-<label>_desc-brain_mask.nii.gz`."""
 
     def __init__(self):
-        super().__init__(p_suffix="mask", p_desc="brain", p_extension=".nii.gz")
+        super().__init__(p_suffix="mask", p_desc="brain", p_extension="nii.gz")
 
 
 class CustomWMMaskBIDSFile(CustomBIDSFile):
     """Represent a custom white-matter mask in the form `sub-<label>_label-WM_dseg.nii.gz`."""
 
     def __init__(self):
-        super().__init__(p_suffix="dseg", p_label="WM", p_extension=".nii.gz")
+        super().__init__(p_suffix="dseg", p_label="WM", p_extension="nii.gz")
 
 
 class CustomGMMaskBIDSFile(CustomBIDSFile):
     """Represent a custom gray-matter mask in the form `sub-<label>_label-GM_dseg.nii.gz`."""
 
     def __init__(self):
-        super().__init__(p_suffix="dseg", p_label="GM", p_extension=".nii.gz")
+        super().__init__(p_suffix="dseg", p_label="GM", p_extension="nii.gz")
 
 
 class CustomCSFMaskBIDSFile(CustomBIDSFile):
     """Represent a custom CSF mask in the form `sub-<label>_label-CSF_dseg.nii.gz`."""
 
     def __init__(self):
-        super().__init__(p_suffix="dseg", p_label="CSF", p_extension=".nii.gz")
+        super().__init__(p_suffix="dseg", p_label="CSF", p_extension="nii.gz")
 
 
 class CustomAparcAsegBIDSFile(CustomBIDSFile):
     """Represent a custom BIDS-formatted Freesurfer aparc+aseg file in the form `sub-<label>_desc-aparcaseg_dseg.nii.gz`."""
 
     def __init__(self):
-        super().__init__(p_suffix="dseg", p_desc="aparcaseg", p_extension=".nii.gz")
+        super().__init__(p_suffix="dseg", p_desc="aparcaseg", p_extension="nii.gz")
diff --git a/cmtklib/carbonfootprint.py b/cmtklib/carbonfootprint.py
new file mode 100644
index 000000000..b805c38ba
--- /dev/null
+++ b/cmtklib/carbonfootprint.py
@@ -0,0 +1,343 @@
+# Copyright (C) 2009-2022, Ecole Polytechnique Federale de Lausanne (EPFL) and
+# Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland, and CMP3 contributors
+# All rights reserved.
+#
+#  This software is distributed under the open-source license Modified BSD.
+
+"""Module that defines CMTK functions for converting C02 emissions estimated with `codecarbon`."""
+
+import os
+from pkg_resources import resource_filename
+import logging
+from pathlib import Path
+import pandas as pd
+from codecarbon import EmissionsTracker
+
+from cmp.info import __version__
+
+
+def create_emissions_tracker(bids_root):
+    """Return a new instance of `codecarbon.EmissionsTracker`.
+    
+    Parameters
+    ----------
+    bids_root : string
+        Path to the root directory of the BIDS dataset
+    
+    Returns
+    -------
+    tracker: `codecarbon.EmissionsTracker`
+        Return a new instance of `codecarbon.EmissionsTracker`
+        
+    References
+    ----------
+    https://github.com/mlco2/codecarbon/blob/v1.2.0/codecarbon/emissions_tracker.py
+    
+    """
+    # Create the code folder if it does not exist yet
+    if not os.path.exists(str(Path(bids_root) / "code")):
+        os.makedirs(str(Path(bids_root) / "code"), exist_ok=True)
+
+    # To not pollute CMP3 outputs with codecarbon outputs
+    # Comment this line for debug if you get for instance
+    # Emissions: O Kg
+    logging.getLogger("codecarbon").disabled = True
+
+    # Create and return the emissions tracker
+    return EmissionsTracker(
+        project_name=f"connectomemapper_{__version__}_gui",
+        output_dir=str(Path(bids_root) / "code"),
+        measure_power_secs=15,
+    )
+
+
+def get_emission_car_miles_equivalent(emissions):
+    """Return the equivalent of CO2 emissions [Kg] in terms of kms traveled by an average car.
+
+    References
+    ----------
+    https://github.com/mlco2/codecarbon/blob/c6aebb9681186a71573748e381b6a3c9731de2d3/codecarbon/viz/data.py#L53
+
+    """
+    return "{:.0f}".format((emissions / 0.409) * 1.60934)
+
+
+def get_emission_tv_time_equivalent(emissions):
+    """Return the equivalent of CO2 emissions [Kg] in terms of kms traveled by an average car.
+
+    References
+    ----------
+    https://github.com/mlco2/codecarbon/blob/c6aebb9681186a71573748e381b6a3c9731de2d3/codecarbon/viz/data.py#L66
+
+    """
+    tv_time_in_minutes = emissions * (1 / 0.097) * 60
+    tv_time = "{:.0f} minutes".format(tv_time_in_minutes)
+    if tv_time_in_minutes >= 60:
+        time_in_hours = tv_time_in_minutes / 60
+        tv_time = "{:.0f} hours".format(time_in_hours)
+        if time_in_hours >= 24:
+            time_in_days = time_in_hours / 24
+            tv_time = "{:.0f} days".format(time_in_days)
+    return tv_time
+
+
+def load_and_compute_carbon_footprint_metrics(emissions_csv_file, nb_of_subjects_processed) -> dict:
+    """Return a dictionary storing the different metrics and variables displayed in the carbon footprint report.
+
+    The dictionary has the different fields:  `'country_name'`, `'region_name'`, `'country_emissions_per_kwh'`,
+    `'duration'`, `'energy_consumed'`, `'emissions'`, `'car_kms'`, `'tv_time'`, `'pred_energy_consumed'`,
+    `'pred_emissions'`, `'pred_car_kms'`, `'pred_tv_time'`.
+
+    Parameters
+    ----------
+    emissions_csv_file : string
+        Path to the `emissions.csv` file generated by `Codecarbon`.
+
+    nb_of_subjects_processed : int
+        Number of subject processed.
+
+    """
+    emissions_df = pd.read_csv(emissions_csv_file)
+    last_index = len(emissions_df) - 1
+    duration = emissions_df['duration'][last_index]
+    energy_consumed = emissions_df['energy_consumed'][last_index]
+    emissions = emissions_df['emissions'][last_index]
+    country_name = emissions_df['country_name'][last_index]
+    region_name = emissions_df['region'][last_index]
+    del emissions_df
+    
+    country_emissions_per_kwh = float(emissions / energy_consumed)
+    car_kms = get_emission_car_miles_equivalent(emissions)
+    tv_time = get_emission_tv_time_equivalent(emissions)
+    pred_duration = 100 * duration / nb_of_subjects_processed
+    pred_energy_consumed = 100 * energy_consumed / nb_of_subjects_processed
+    pred_emissions = 100 * emissions / nb_of_subjects_processed
+    pred_car_kms = get_emission_car_miles_equivalent(pred_emissions)
+    pred_tv_time = get_emission_tv_time_equivalent(pred_emissions)
+    
+    carbon_footprint_metrics = {
+        'country_name': f'{country_name}',
+        'region_name': f'{region_name}',
+        'country_emissions_per_kwh': f'{country_emissions_per_kwh}',
+        'duration': f'{duration}',
+        'energy_consumed': f'{energy_consumed}',
+        'emissions': f'{emissions}',
+        'car_kms': f'{car_kms}',
+        'tv_time': f'{tv_time}',
+        'pred_duration': f'{pred_duration}',
+        'pred_energy_consumed': f'{pred_energy_consumed}',
+        'pred_emissions': f'{pred_emissions}',
+        'pred_car_kms': f'{pred_car_kms}',
+        'pred_tv_time': f'{pred_tv_time}',
+    }
+    return carbon_footprint_metrics
+
+
+def create_carbon_footprint_message(bids_dir, emissions_csv_file, nb_of_subjects_processed):
+    """Return a string containg the carbon footprint print message to be passed to `print()`.
+
+    Parameters
+    ----------
+    bids_dir : string
+        Path to root directory of the BIDS dataset
+ 
+    emissions_csv_file : string
+        Path to the `emissions.csv` file generated by `Codecarbon`.
+
+    nb_of_subjects_processed : int
+        Number of subject processed.
+
+    Returns
+    -------
+    carbon_footprint_msg : string
+        String formatted containing the carbon footprint meassge to be passed to `print()`
+
+    """
+    carbon_footprint_metrics = load_and_compute_carbon_footprint_metrics(
+        emissions_csv_file=emissions_csv_file,
+        nb_of_subjects_processed=nb_of_subjects_processed
+    )
+    carbon_footprint_msg = "#" * 80 + "\n"
+    carbon_footprint_msg += f"CARBON FOOTPRINT REPORT\n"
+    carbon_footprint_msg += "#" * 80 + "\n"
+    carbon_footprint_msg += "Carbon footprint results\n"
+    carbon_footprint_msg += "-" * 80 + "\n"
+    carbon_footprint_msg += f"Connectome Mapper ({__version__}) was run on {nb_of_subjects_processed} subject(s) "
+    carbon_footprint_msg += f"in {carbon_footprint_metrics['region_name']} ({carbon_footprint_metrics['country_name']})"
+    carbon_footprint_msg += f" (Mean CO<sub>2</sub> kg / kWH: {carbon_footprint_metrics['country_emissions_per_kwh']}),"
+    carbon_footprint_msg += " having the following estimated carbon footprint:\n"
+    carbon_footprint_msg += f"\t* Duration: {carbon_footprint_metrics['duration']} s\n"
+    carbon_footprint_msg += f"\t* Energy consumed: {carbon_footprint_metrics['energy_consumed']} kWh\n"
+    carbon_footprint_msg += f"\t* Estimated Co2 emissions: {carbon_footprint_metrics['emissions']} kg\n"
+    carbon_footprint_msg += "\t* Equivalent in distance travelled by "
+    carbon_footprint_msg += f"avg car: {carbon_footprint_metrics['car_kms']} kms\n"
+    carbon_footprint_msg += "\t* Equivalent in amount of time watching a 32-inch LCD flat "
+    carbon_footprint_msg += f"screen TV: {carbon_footprint_metrics['tv_time']}\n"
+    carbon_footprint_msg += "#" * 80 + "\n"
+    carbon_footprint_msg += f"Carbon footprint prediction for 100 subjects in the same conditions\n"
+    carbon_footprint_msg += "-" * 80 + "\n"
+    carbon_footprint_msg += f"\t* Predicted duration: {carbon_footprint_metrics['pred_duration']} s\n"
+    carbon_footprint_msg += f"\t* Predicted energy consumed: {carbon_footprint_metrics['pred_energy_consumed']} kWh\n"
+    carbon_footprint_msg += f"\t* Predicted Co2 emissions: {carbon_footprint_metrics['pred_emissions']} kg\n"
+    carbon_footprint_msg += "\t* Equivalent in distance travelled by "
+    carbon_footprint_msg += f"avg car: {carbon_footprint_metrics['pred_car_kms']} kms\n"
+    carbon_footprint_msg += "\t* Equivalent in amount of time watching a 32-inch LCD flat "
+    carbon_footprint_msg += f"screen TV: {carbon_footprint_metrics['pred_tv_time']}\n"
+    carbon_footprint_msg += "#" * 80 + "\n"
+    carbon_footprint_msg += "Results can be visualized with the codecarbon visualization "
+    carbon_footprint_msg += "tool using following command:\n\n"
+    carbon_footprint_msg += f'\t$ carbonboard --filepath="{bids_dir}/code/emissions.csv" --port=9999\n'
+    return carbon_footprint_msg
+
+
+def create_html_carbon_footprint_report(emissions_csv_file, nb_of_subjects_processed):
+    """Return a string containing the content of html report to be passed to traits `Str` with `HTMLEditor`.
+    
+    Parameters
+    ----------
+    emissions_csv_file : string
+        Path to the `emissions.csv` file generated by `Codecarbon`.
+
+    nb_of_subjects_processed : int
+        Number of subject processed.
+    """
+    carbon_footprint_metrics = load_and_compute_carbon_footprint_metrics(
+        emissions_csv_file=emissions_csv_file,
+        nb_of_subjects_processed=nb_of_subjects_processed
+    )
+    # Get path to different resources used in the <head> of the HTML document
+    resources_dir = os.path.join('data', 'report', 'carbonfootprint')
+    jquery_js_file = resource_filename('cmtklib', os.path.join(resources_dir, 'js', 'jquery.3.3.1.min.js'))
+    bootstrap_css_file = resource_filename(
+        'cmtklib', os.path.join(resources_dir, 'css', 'bootstrap-combined.no-icons.min.css')
+    )
+
+    return f"""
+<!DOCTYPE html>
+<html>
+<head>
+  <title>Footer</title>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <script src="{jquery_js_file}"></script>
+  <link href="{bootstrap_css_file}" rel="stylesheet">
+  <script src="https://kit.fontawesome.com/d2ef6e0082.js" crossorigin="anonymous"></script>
+
+  <style>
+    div {{
+      border: 1px solid gray;
+      padding: 8px;
+    }}
+
+    h1 {{
+      text-align: center;
+      text-transform: uppercase;
+      color: #4CAF50;
+    }}
+
+    p {{
+      margin: 0px 10px 0px 10px;
+      padding: 10px 10px 10px 10px;
+      text-indent: 0px;
+      text-align: justify;
+      background-color: #EEEEEE;
+    }}
+
+    a {{
+      text-decoration: none;
+      color: #008CBA;
+    }}
+    
+    #footer {{
+      border: 0px solid gray;
+      padding: 8px;
+    }}
+
+    #GFG {{
+      border: 0px solid gray;
+      padding: 8px;
+      height: 60px;
+      text-align: center;
+      padding: 3px;
+      color: white;
+      background-image: url(https://ohbm-environment.org/wp-content/uploads/slider/cache/aceabfbee23a7b3e8e9fed910c639555/Borneo_rainforest-3.jpg);
+      background-position: center center;
+      background-repeat: no-repeat;
+      background-size: cover;
+    }}
+    .fa-brain{{
+      color: pink;
+      font-size: 1em;
+      margin: 0px 10px 0px 10px;
+      vertical-align: middle;
+      horizontal-align: left;
+    }}
+  </style>
+</head>
+<body>
+    <div id="GFG">
+    </div>
+    <div>
+      <h4>
+          Carbon footprint results
+      </h4>
+      <p>
+          Connectome Mapper ({__version__}) was run on {nb_of_subjects_processed} subject(s)
+          in {carbon_footprint_metrics['region_name']} ({carbon_footprint_metrics['country_name']})
+          (Mean CO<sub>2</sub> kg / kWH: {carbon_footprint_metrics['country_emissions_per_kwh']}), having
+          the following estimated carbon footprint:
+      </p>
+      <ul>
+          <li>Total run time: {carbon_footprint_metrics['duration']}s </li>
+          <li>Total energy consumed: {carbon_footprint_metrics['energy_consumed']} kWh </li>
+          <li>Total estimated CO<sub>2</sub> emissions: {carbon_footprint_metrics['emissions']} kg </li>
+          <li>
+            Equivalent in distance travelled by avg
+            <i class="fas fa-car"></i>: {carbon_footprint_metrics['car_kms']} kms
+          </li>
+          <li>
+            Equivalent in amount of time watching a 32-inch LCD flat screen
+            <i class="fas fa-tv"></i>: {carbon_footprint_metrics['tv_time']}
+          </li>
+      </ul>
+      <p>
+        <em>
+            Estimations were conducted using the
+            <a href="https://github.com/mlco2/codecarbon">CodeCarbon emissions tracker</a>.
+        </em>
+      </p>
+      <h4>
+          Carbon footprint prediction for 100 subjects
+      </h4>
+      <p>
+          In the same conditions, this would have resulted in:
+      </p>
+      <ul>
+          <li>Total run time: {carbon_footprint_metrics['pred_duration']}s </li>
+          <li>Total energy consumed: {carbon_footprint_metrics['pred_energy_consumed']} kWh </li>
+          <li>Co2 emissions: {carbon_footprint_metrics['pred_emissions']} kg</li>
+          <li>
+            Equivalent in distance travelled by avg
+            <i class="fas fa-car"></i>: {carbon_footprint_metrics['pred_car_kms']} kms
+          </li>
+          <li>
+            Equivalent in amount of time watching a 32-inch LCD flat screen
+            <i class="fas fa-tv"></i>: {carbon_footprint_metrics['pred_tv_time']}
+          </li>
+      </ul>
+    </div>
+</body>
+<footer>
+  <div id="footer">
+    <p>
+        Actively part of the initiative created by the
+        <a href="https://neuropipelines.github.io/20pipelines">
+            Sustainability and Environment Action Special Interest Group</a>,
+        the CMP developers hope that by providing you with such metrics it can allow you to be more aware about
+        the carbon footprint of your<i class="fas fa-brain" aria-hidden= "true"></i>research. &#127757; &#10024;
+    </p>
+  </div>
+</footer>
+<html>
+
+    """
diff --git a/cmtklib/data/report/carbonfootprint/css/bootstrap-combined-no-icons.2.3.2.min.css b/cmtklib/data/report/carbonfootprint/css/bootstrap-combined-no-icons.2.3.2.min.css
new file mode 100644
index 000000000..5ab243ec7
--- /dev/null
+++ b/cmtklib/data/report/carbonfootprint/css/bootstrap-combined-no-icons.2.3.2.min.css
@@ -0,0 +1,732 @@
+/*!
+ * Bootstrap v2.3.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
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+.thumbnail{display:block;padding:4px;line-height:20px;border:1px solid #ddd;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.055);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.055);box-shadow:0 1px 3px rgba(0, 0, 0, 0.055);-webkit-transition:all 0.2s ease-in-out;-moz-transition:all 0.2s ease-in-out;-o-transition:all 0.2s ease-in-out;transition:all 0.2s ease-in-out;}
+a.thumbnail:hover,a.thumbnail:focus{border-color:#0088cc;-webkit-box-shadow:0 1px 4px rgba(0, 105, 214, 0.25);-moz-box-shadow:0 1px 4px rgba(0, 105, 214, 0.25);box-shadow:0 1px 4px rgba(0, 105, 214, 0.25);}
+.thumbnail>img{display:block;max-width:100%;margin-left:auto;margin-right:auto;}
+.thumbnail .caption{padding:9px;color:#555555;}
+.alert{padding:8px 35px 8px 14px;margin-bottom:20px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#fcf8e3;border:1px solid #fbeed5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}
+.alert,.alert h4{color:#c09853;}
+.alert h4{margin:0;}
+.alert .close{position:relative;top:-2px;right:-21px;line-height:20px;}
+.alert-success{background-color:#dff0d8;border-color:#d6e9c6;color:#468847;}
+.alert-success h4{color:#468847;}
+.alert-danger,.alert-error{background-color:#f2dede;border-color:#eed3d7;color:#b94a48;}
+.alert-danger h4,.alert-error h4{color:#b94a48;}
+.alert-info{background-color:#d9edf7;border-color:#bce8f1;color:#3a87ad;}
+.alert-info h4{color:#3a87ad;}
+.alert-block{padding-top:14px;padding-bottom:14px;}
+.alert-block>p,.alert-block>ul{margin-bottom:0;}
+.alert-block p+p{margin-top:5px;}
+@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-o-keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}@keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}.progress{overflow:hidden;height:20px;margin-bottom:20px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#fff9f9f9', GradientType=0);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}
+.progress .bar{width:0%;height:100%;color:#ffffff;float:left;font-size:12px;text-align:center;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(to bottom, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff149bdf', endColorstr='#ff0480be', GradientType=0);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;}
+.progress .bar+.bar{-webkit-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);-moz-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);}
+.progress-striped .bar{background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;}
+.progress.active .bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;-ms-animation:progress-bar-stripes 2s linear infinite;-o-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite;}
+.progress-danger .bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0);}
+.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);}
+.progress-success .bar,.progress .bar-success{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(to bottom, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff62c462', endColorstr='#ff57a957', GradientType=0);}
+.progress-success.progress-striped .bar,.progress-striped .bar-success{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);}
+.progress-info .bar,.progress .bar-info{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(to bottom, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff339bb9', GradientType=0);}
+.progress-info.progress-striped .bar,.progress-striped .bar-info{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);}
+.progress-warning .bar,.progress .bar-warning{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(to bottom, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450', endColorstr='#fff89406', GradientType=0);}
+.progress-warning.progress-striped .bar,.progress-striped .bar-warning{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);}
+.hero-unit{padding:60px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:30px;color:inherit;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;}
+.hero-unit li{line-height:30px;}
+.media,.media-body{overflow:hidden;*overflow:visible;zoom:1;}
+.media,.media .media{margin-top:15px;}
+.media:first-child{margin-top:0;}
+.media-object{display:block;}
+.media-heading{margin:0 0 5px;}
+.media>.pull-left{margin-right:10px;}
+.media>.pull-right{margin-left:10px;}
+.media-list{margin-left:0;list-style:none;}
+.tooltip{position:absolute;z-index:1030;display:block;visibility:visible;font-size:11px;line-height:1.4;opacity:0;filter:alpha(opacity=0);}.tooltip.in{opacity:0.8;filter:alpha(opacity=80);}
+.tooltip.top{margin-top:-3px;padding:5px 0;}
+.tooltip.right{margin-left:3px;padding:0 5px;}
+.tooltip.bottom{margin-top:3px;padding:5px 0;}
+.tooltip.left{margin-left:-3px;padding:0 5px;}
+.tooltip-inner{max-width:200px;padding:8px;color:#ffffff;text-align:center;text-decoration:none;background-color:#000000;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}
+.tooltip-arrow{position:absolute;width:0;height:0;border-color:transparent;border-style:solid;}
+.tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-width:5px 5px 0;border-top-color:#000000;}
+.tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-width:5px 5px 5px 0;border-right-color:#000000;}
+.tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-width:5px 0 5px 5px;border-left-color:#000000;}
+.tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-width:0 5px 5px;border-bottom-color:#000000;}
+.popover{position:absolute;top:0;left:0;z-index:1010;display:none;max-width:276px;padding:1px;text-align:left;background-color:#ffffff;-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);white-space:normal;}.popover.top{margin-top:-10px;}
+.popover.right{margin-left:10px;}
+.popover.bottom{margin-top:10px;}
+.popover.left{margin-left:-10px;}
+.popover-title{margin:0;padding:8px 14px;font-size:14px;font-weight:normal;line-height:18px;background-color:#f7f7f7;border-bottom:1px solid #ebebeb;-webkit-border-radius:5px 5px 0 0;-moz-border-radius:5px 5px 0 0;border-radius:5px 5px 0 0;}.popover-title:empty{display:none;}
+.popover-content{padding:9px 14px;}
+.popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid;}
+.popover .arrow{border-width:11px;}
+.popover .arrow:after{border-width:10px;content:"";}
+.popover.top .arrow{left:50%;margin-left:-11px;border-bottom-width:0;border-top-color:#999;border-top-color:rgba(0, 0, 0, 0.25);bottom:-11px;}.popover.top .arrow:after{bottom:1px;margin-left:-10px;border-bottom-width:0;border-top-color:#ffffff;}
+.popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0, 0, 0, 0.25);}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#ffffff;}
+.popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0, 0, 0, 0.25);top:-11px;}.popover.bottom .arrow:after{top:1px;margin-left:-10px;border-top-width:0;border-bottom-color:#ffffff;}
+.popover.left .arrow{top:50%;right:-11px;margin-top:-11px;border-right-width:0;border-left-color:#999;border-left-color:rgba(0, 0, 0, 0.25);}.popover.left .arrow:after{right:1px;border-right-width:0;border-left-color:#ffffff;bottom:-10px;}
+.modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040;background-color:#000000;}.modal-backdrop.fade{opacity:0;}
+.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);}
+.modal{position:fixed;top:10%;left:50%;z-index:1050;width:560px;margin-left:-280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;outline:none;}.modal.fade{-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;top:-25%;}
+.modal.fade.in{top:10%;}
+.modal-header{padding:9px 15px;border-bottom:1px solid #eee;}.modal-header .close{margin-top:2px;}
+.modal-header h3{margin:0;line-height:30px;}
+.modal-body{position:relative;overflow-y:auto;max-height:400px;padding:15px;}
+.modal-form{margin-bottom:0;}
+.modal-footer{padding:14px 15px 15px;margin-bottom:0;text-align:right;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";line-height:0;}
+.modal-footer:after{clear:both;}
+.modal-footer .btn+.btn{margin-left:5px;margin-bottom:0;}
+.modal-footer .btn-group .btn+.btn{margin-left:-1px;}
+.modal-footer .btn-block+.btn-block{margin-left:0;}
+.dropup,.dropdown{position:relative;}
+.dropdown-toggle{*margin-bottom:-3px;}
+.dropdown-toggle:active,.open .dropdown-toggle{outline:0;}
+.caret{display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";}
+.dropdown .caret{margin-top:8px;margin-left:2px;}
+.dropdown-menu{position:absolute;top:100%;left:0;z-index:1000;display:none;float:left;min-width:160px;padding:5px 0;margin:2px 0 0;list-style:none;background-color:#ffffff;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);*border-right-width:2px;*border-bottom-width:2px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;}.dropdown-menu.pull-right{right:0;left:auto;}
+.dropdown-menu .divider{*width:100%;height:1px;margin:9px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;}
+.dropdown-menu>li>a{display:block;padding:3px 20px;clear:both;font-weight:normal;line-height:20px;color:#333333;white-space:nowrap;}
+.dropdown-menu>li>a:hover,.dropdown-menu>li>a:focus,.dropdown-submenu:hover>a,.dropdown-submenu:focus>a{text-decoration:none;color:#ffffff;background-color:#0081c2;background-image:-moz-linear-gradient(top, #0088cc, #0077b3);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0077b3));background-image:-webkit-linear-gradient(top, #0088cc, #0077b3);background-image:-o-linear-gradient(top, #0088cc, #0077b3);background-image:linear-gradient(to bottom, #0088cc, #0077b3);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0077b3', GradientType=0);}
+.dropdown-menu>.active>a,.dropdown-menu>.active>a:hover,.dropdown-menu>.active>a:focus{color:#ffffff;text-decoration:none;outline:0;background-color:#0081c2;background-image:-moz-linear-gradient(top, #0088cc, #0077b3);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0077b3));background-image:-webkit-linear-gradient(top, #0088cc, #0077b3);background-image:-o-linear-gradient(top, #0088cc, #0077b3);background-image:linear-gradient(to bottom, #0088cc, #0077b3);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff0088cc', endColorstr='#ff0077b3', GradientType=0);}
+.dropdown-menu>.disabled>a,.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{color:#999999;}
+.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:default;}
+.open{*z-index:1000;}.open>.dropdown-menu{display:block;}
+.dropdown-backdrop{position:fixed;left:0;right:0;bottom:0;top:0;z-index:990;}
+.pull-right>.dropdown-menu{right:0;left:auto;}
+.dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000000;content:"";}
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diff --git a/conda/environment.yml b/conda/environment.yml
index e4bb4412c..b5ed975b5 100644
--- a/conda/environment.yml
+++ b/conda/environment.yml
@@ -1,38 +1,38 @@
 name: py37cmp-gui
 
 channels:
-- conda-forge
-- aramislab
-- mrtrix3
+    - conda-forge
+    - aramislab
+    - mrtrix3
+    - anaconda
 
 dependencies:
-- python=3.7
-- pip=20.1.1
-- numpy=1.19.2 #
-- matplotlib=3.2.2 # =2.2.3
-- traits=6.2.0 # =5.1
-- traitsui=7.0.0 # =6.0.0
-- graphviz=2.40.1 # =2.40.1
-- configparser=5.0.0
-- nipype=1.7.0 # =1.5.0
-- git-annex=8.20210127 # =7.20190219
-- pyside2=5.9.0a1 # =5.9.0a1
-- fslpy=3.2.1 # =1.13.2
-- fsleyes=0.33.0 # =0.27.3
-- indexed_gzip=1.2.0 # requirements of fsleyes
-- dipy=1.3.0
-- cvxpy-base=1.1.7
-- cvxpy=1.1.7
-- obspy=1.2.2
-- mrtrix3=3.0.2
+    - python=3.7
+    - pip=21.3.1
+    - numpy=1.21.5
+    - matplotlib=3.5.1
+    - traits=6.3.2
+    - traitsui=7.2.0
+    - graphviz=2.50.0
+    - configparser=5.2.0
+    - nipype=1.7.0
+    - git-annex=8.20211123
+    - pyside2=5.13.2
+    - indexed_gzip=1.6.4
+    - dipy=1.3.0
+    - cvxpy-base=1.1.18
+    - cvxpy=1.1.18
+    - fsleyes=1.3.3
+    - mrtrix3=3.0.3
 
-- pip:
-    - duecredit==0.8.0 # ==0.7.0
-    - mne==0.20.7 # ==0.17.1
-    - datalad[full]==0.14.0 # ==0.11.4
-    - datalad-container==1.1.2
-    - datalad-neuroimaging==0.3.1
-    - pybids==0.14.0 # ==0.9.5
-    - statsmodels==0.11.1 # ==0.9.0
-    - networkx==2.4
-    - pydicom==2.0.0 # ==1.4.2
+    - pip:
+          - duecredit==0.9.1
+          - obspy==1.2.2
+          - mne==0.24.1
+          - datalad[full]==0.15.4
+          - datalad-container==1.1.5
+          - datalad-neuroimaging==0.3.1
+          - pybids==0.14.0
+          - statsmodels==0.13.1
+          - networkx==2.6.3
+          - pydicom==2.2.2
diff --git a/conda/environment_macosx.yml b/conda/environment_macosx.yml
index 8ab006a8c..f2bb1861f 100644
--- a/conda/environment_macosx.yml
+++ b/conda/environment_macosx.yml
@@ -1,38 +1,37 @@
 name: py37cmp-gui
 
 channels:
-- conda-forge
-- aramislab
-- mrtrix3
+    - conda-forge
+    - aramislab
+    - mrtrix3
+    - anaconda
 
 dependencies:
-- python=3.7
-- pip=20.1.1
-- numpy=1.19.2
-- matplotlib=3.2.2  # 2.2.3
-- graphviz=2.40.1
-- traits=6.2.0
-- traitsui=7.0.0
-- configparser=5.0.0
-- nipype=1.7.0
-- pyside2=5.9.0a1
-- pydotplus=2.0.2
-- fslpy=3.2.1 # =1.13.2
-- fsleyes=0.33.0 # =0.27.3
-- indexed_gzip=1.2.0 # requirements of fsleyes
-- dipy=1.3.0
-- cvxpy-base=1.1.7
-- cvxpy=1.1.7
-- obspy=1.2.2
-- mrtrix3=3.0.2
+    - python=3.7
+    - pip=21.3.1
+    - numpy=1.21.5
+    - matplotlib=3.5.1
+    - traits=6.3.2
+    - traitsui=7.2.0
+    - graphviz=2.50.0
+    - configparser=5.2.0
+    - nipype=1.7.0
+    - pyside2=5.13.2
+    - indexed_gzip=1.6.4
+    - dipy=1.3.0
+    - cvxpy-base=1.1.18
+    - cvxpy=1.1.18
+    - fsleyes=1.3.3
+    - mrtrix3=3.0.3
 
-- pip:
-    - duecredit==0.8.0  # 0.7.0
-    - mne==0.20.7  # 0.17.1
-    - datalad[full]==0.14.0  # 0.11.3
-    - datalad-container==1.1.2
-    - datalad_neuroimaging==0.3.1
-    - pybids==0.14.0  # 0.9.1
-    - statsmodels==0.11.1  # 0.9.0
-    - networkx==2.4
-    - pydicom==2.0.0  # 1.4.2
+    - pip:
+          - duecredit==0.9.1
+          - obspy==1.2.2
+          - mne==0.24.1
+          - datalad[full]==0.15.4
+          - datalad-container==1.1.5
+          - datalad-neuroimaging==0.3.1
+          - pybids==0.14.0
+          - statsmodels==0.13.1
+          - networkx==2.6.3
+          - pydicom==2.2.2
diff --git a/run.py b/run.py
index a3a63968b..9bf31530f 100644
--- a/run.py
+++ b/run.py
@@ -530,8 +530,7 @@ def run(command, env={}, log_filename={}):
                 print("        - Anatomical MRI (segmentation and parcellation)")
 
                 if args.dwi_pipeline_config is not None:
-                    print(
-                        "        - Diffusion MRI (structural connectivity matrices)")
+                    print("        - Diffusion MRI (structural connectivity matrices)")
 
                 if args.func_pipeline_config is not None:
                     print("        - fMRI (functional connectivity matrices)")
@@ -557,7 +556,11 @@ def run(command, env={}, log_filename={}):
                                              run_fmri=run_fmri,
                                              number_of_threads=number_of_threads)
                     print_blue("... cmd : {}".format(cmd))
-
+                    if project.subject_session != "":
+                        log_file = '{}_{}_log.txt'.format(project.subject,
+                                                          project.subject_session)
+                    else:
+                        log_file = '{}_log.txt'.format(project.subject)
                     proc = run(command=cmd, env={},
                                log_filename=os.path.join(project.output_directory, __cmp_directory__,
                                                          project.subject, project.subject_session,
diff --git a/setup.py b/setup.py
index 68cb1eca2..b9af87648 100644
--- a/setup.py
+++ b/setup.py
@@ -86,6 +86,8 @@ def run(self):
         "data/segmentation/ants_MICCAI2012_multi-atlas_challenge_data/*/*.*",
         "data/segmentation/ants_MICCAI2012_multi-atlas_challenge_data/*.*",
         "data/segmentation/thalamus2018/*.*",
+        "data/report/carbonfootprint/css/*.*",
+        "data/report/carbonfootprint/js/*.*",
     ],
 }
 
@@ -118,8 +120,11 @@ def run(self):
                 dependency_links.append(line)
                 # Adds package name to dependencies
                 install_requires.append(line)
-print(f"Install requires: {install_requires}")
-print(f"Dependency links: {dependency_links}")
+# Install automatically codecarbon with CMP3
+install_requires.append('codecarbon==1.2.0')
+install_requires.append('dash-bootstrap-components==0.13.1')
+print(f'Install requires: {install_requires}')
+print(f'Dependency links: {dependency_links}')
 
 
 # Read the contents of your README file
diff --git a/setup_pypi.py b/setup_pypi.py
index 02ce8d0e0..67cd83e51 100644
--- a/setup_pypi.py
+++ b/setup_pypi.py
@@ -77,6 +77,10 @@ def run(self):
         "pipelines/functional/*.png",
     ],
     "resources": ["buttons/*.png", "icons/*png"],
+    "cmtklib": [
+        "data/report/carbonfootprint/css/*.*",
+        "data/report/carbonfootprint/js/*.*",
+    ],
 }
 
 # Extract package requirements from Conda environment.yml
@@ -108,8 +112,11 @@ def run(self):
                 dependency_links.append(line)
                 # Adds package name to dependencies
                 install_requires.append(line)
-print(f"Install requires: {install_requires}")
-print(f"Dependency links: {dependency_links}")
+# Install automatically codecarbon with CMP3
+install_requires.append('codecarbon==1.2.0')
+install_requires.append('dash-bootstrap-components==0.13.1')
+print(f'Install requires: {install_requires}')
+print(f'Dependency links: {dependency_links}')
 
 
 # Read the contents of your README file


Test patch:
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt
index e28021c9d..dc3fd9848 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt
@@ -1,43 +1,43 @@
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/dataset_description.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
@@ -414,31 +414,6 @@ nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_vo
 nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/scale4_roi_stats.tsv
 nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/scale5_roi_stats.tsv
 nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_inputs.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile0/_inputs.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile0/_node.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile0/_report/report.rst
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile0/result__createBIDSLabelIndexMappingFile0.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile0/ROIv_Lausanne2018_scale1.tsv
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile1/_inputs.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile1/_node.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile1/_report/report.rst
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile1/result__createBIDSLabelIndexMappingFile1.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile1/ROIv_Lausanne2018_scale2.tsv
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile2/_inputs.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile2/_node.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile2/_report/report.rst
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile2/result__createBIDSLabelIndexMappingFile2.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile2/ROIv_Lausanne2018_scale3.tsv
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile3/_inputs.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile3/_node.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile3/_report/report.rst
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile3/result__createBIDSLabelIndexMappingFile3.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile3/ROIv_Lausanne2018_scale4.tsv
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile4/_inputs.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile4/_node.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile4/_report/report.rst
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile4/result__createBIDSLabelIndexMappingFile4.pklz
-nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/mapflow/_createBIDSLabelIndexMappingFile4/ROIv_Lausanne2018_scale5.tsv
 nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_node.pklz
 nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_report/report.rst
 nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/result_createBIDSLabelIndexMappingFile.pklz
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt
index cc06c2ddc..dc398db5a 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt
@@ -1,22 +1,22 @@
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/dataset_description.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt
index 6ead5f5b7..901ebe96c 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt
@@ -38,44 +38,44 @@ cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
 cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
 cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
 cmp-custom/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.graphml
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
-cmp-v3.0.1/sub-01/ses-01/xfm/sub-01_ses-01_space-DWI_desc-head_T1w.mat
+cmp-v3.0.2/dataset_description.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.graphml
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
+cmp-v3.0.2/sub-01/ses-01/xfm/sub-01_ses-01_space-DWI_desc-head_T1w.mat
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt
index ab0e22080..322d5f02d 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt
@@ -1,79 +1,79 @@
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GMWMI_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-PROB_tractogram.trk
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
-cmp-v3.0.1/sub-01/ses-01/xfm/final0GenericAffine.mat
-cmp-v3.0.1/sub-01/ses-01/xfm/final1Warp.nii.gz
+cmp-v3.0.2/dataset_description.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GMWMI_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-PROB_tractogram.trk
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
+cmp-v3.0.2/sub-01/ses-01/xfm/final0GenericAffine.mat
+cmp-v3.0.2/sub-01/ses-01/xfm/final1Warp.nii.gz
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt
index 5a9f8eb0c..4cc2102cf 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt
@@ -1,81 +1,81 @@
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-CSF_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GM_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
-cmp-v3.0.1/sub-01/ses-01/xfm/final0GenericAffine.mat
-cmp-v3.0.1/sub-01/ses-01/xfm/final1Warp.nii.gz
+cmp-v3.0.2/dataset_description.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-CSF_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GM_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
+cmp-v3.0.2/sub-01/ses-01/xfm/final0GenericAffine.mat
+cmp-v3.0.2/sub-01/ses-01/xfm/final1Warp.nii.gz
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt
index b32cf198c..b5997df9a 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt
@@ -1,81 +1,81 @@
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-CSF_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GM_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_probseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-PROB_tractogram.trk
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
-cmp-v3.0.1/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
-cmp-v3.0.1/sub-01/ses-01/xfm/final0GenericAffine.mat
-cmp-v3.0.1/sub-01/ses-01/xfm/final1Warp.nii.gz
+cmp-v3.0.2/dataset_description.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-CSF_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GM_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_probseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json
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+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-PROB_tractogram.trk
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_diffusion_config.json
+cmp-v3.0.2/sub-01/ses-01/xfm/final0GenericAffine.mat
+cmp-v3.0.2/sub-01/ses-01/xfm/final1Warp.nii.gz
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt
index 0bb5075c4..7e40a234a 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt
@@ -1,87 +1,87 @@
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
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-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
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-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
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-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
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-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale3_dseg.nii.gz
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-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.graphml
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_timeseries.mat
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.mat
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_timeseries.mat
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_timeseries.npy
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.graphml
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.mat
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_timeseries.mat
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.graphml
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.mat
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_timeseries.mat
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.graphml
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_timeseries.mat
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_meanBOLD.nii.gz
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-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-bandpass_bold.nii.gz
-cmp-v3.0.1/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.json
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-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_fMRI_config.json
+cmp-v3.0.2/dataset_description.json
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+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
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+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
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+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
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+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_fMRI_config.json
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt
index cd008ebfa..311545d3d 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt
@@ -1,83 +1,83 @@
-cmp-v3.0.1/dataset_description.json
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-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
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+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz
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+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_timeseries.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_timeseries.npy
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_timeseries.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_timeseries.npy
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_timeseries.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_timeseries.npy
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_timeseries.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_timeseries.npy
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_timeseries.mat
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_timeseries.npy
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_meanBOLD.nii.gz
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_motion.tsv
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-bandpass_bold.nii.gz
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.json
+cmp-v3.0.2/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_fMRI_config.json
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt
index 04d4ef442..dc3fd9848 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt
@@ -1,43 +1,43 @@
-cmp-v3.0.1/dataset_description.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.1/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.2/dataset_description.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp-v3.0.2/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
 freesurfer-6.0.1/dataset_description.json
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-6.0.1/sub-01_ses-01/label/aparc.annot.ctab