Repository: connectomicslab/connectomemapper3 (language: python)

Issue:
Dipy tracking with DTI model does not work anymore
**How it happened**
After updating to Dipy 1.0.

**How to solve**
Need to update code for Dipy tracking with DTI model following major changes in Dipy 1.0. 

> The EuDX tracking function has been removed. EuDX tractography can be performed using ``dipy.tracking.local_tracking`` using ``dipy.reconst.peak_direction_getter.EuDXDirectionGetter``.

from https://www.dipy.org/documentation/1.3.0./api_changes/#dipy-1-0-0-changes


Discussion / hints:

Fix patch:
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7a6ff9b04..c0b827acb 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,7 +1,7 @@
 version: 2.1
 
 orbs:
-  coverage-reporter: codacy/coverage-reporter@11.0.1
+  coverage-reporter: codacy/coverage-reporter@11.9.0
   singularity: singularity/singularity@1.0.10
 
 jobs:
@@ -327,6 +327,36 @@ jobs:
             sudo find /tmp/data/${CIRCLE_JOB}/ds-sample/derivatives -path */figures -prune -o -not -name "_*.json" -type f -print | sed s+/tmp/data/${CIRCLE_JOB}/ds-sample/derivatives/++ | sort > /tmp/data/ds-sample/test/test-02_outputs.out
             diff /home/circleci/src/connectomemapper3/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt /tmp/data/ds-sample/test/test-02_outputs.out
             exit $?
+      - run:
+          name: Run anatomical and diffusion pipelines on ds-sample (test 9 - Lausanne2018 + FSL FLIRT + Dipy SHORE + MRtrix SD_Stream tracking + MRtrix SIFT tractogram filtering)
+          no_output_timeout: 8h
+          command: |
+            # Execute BIDS App
+            docker run -it --rm \
+            --entrypoint /app/run_coverage_cmp3.sh \
+            -v /tmp/data/${CIRCLE_JOB}/ds-sample:/bids_dir \
+            -v /tmp/data/${CIRCLE_JOB}/ds-sample/derivatives:/output_dir \
+            -v /home/circleci/src/connectomemapper3/.circleci/tests/configuration_files:/config \
+            sebastientourbier/connectomemapper3 \
+            /bids_dir /output_dir participant --participant_label 01 --session_label 01 \
+            --anat_pipeline_config /config/ref_anatomical_config_1.ini \
+            --dwi_pipeline_config /config/ref_diffusion_config_5.ini \
+            --fs_license /bids_dir/code/license.txt \
+            --coverage
+
+            # Rename partial coverage
+            mv /tmp/data/${CIRCLE_JOB}/ds-sample/code/coverage.xml /tmp/data/ds-sample/test/test-09_coverage.xml
+
+            # Rename execution log
+            mv /tmp/data/${CIRCLE_JOB}/ds-sample/code/log.txt /tmp/data/ds-sample/test/test-09_log.txt
+      - run:
+          name: Checking outputs of Connectome Mapper run (test 9)
+          command: |
+            # Get all files in derivatives except the _*.json interface hash generated by nipype (find) /
+            # Remove the full path of the derivatives (sed) / sort the files and write it to a text file
+            sudo find /tmp/data/${CIRCLE_JOB}/ds-sample/derivatives -path */figures -prune -o -not -name "_*.json" -type f -print | sed s+/tmp/data/${CIRCLE_JOB}/ds-sample/derivatives/++ | sort > /tmp/data/ds-sample/test/test-09_outputs.out
+            diff /home/circleci/src/connectomemapper3/.circleci/tests/expected_outputs/ds-sample_test-09_outputs.txt /tmp/data/ds-sample/test/test-09_outputs.out
+            exit $?
       - persist_to_workspace:
           root: /tmp
           paths:
@@ -676,8 +706,38 @@ jobs:
             # Get all files in derivatives except the _*.json interface hash generated by nipype (find) /
             # Remove the full path of the derivatives (sed) / sort the files and write it to a text file
             sudo find /tmp/data/${CIRCLE_JOB}/ds-sample/derivatives -path */figures -prune -o -not -name "_*.json" -type f -print | sed s+/tmp/data/${CIRCLE_JOB}/ds-sample/derivatives/++ | sort > /tmp/data/ds-sample/test/test-07_outputs.out
-            # diff /home/circleci/src/connectomemapper3/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt /tmp/data/ds-sample/test/test-07_outputs.out
-            # exit $?
+            diff /home/circleci/src/connectomemapper3/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt /tmp/data/ds-sample/test/test-07_outputs.out
+            exit $?
+      - run:
+          name: Run anatomical and fmri pipelines on ds-sample (test 8 - Lausanne2018 + FSL FLIRT + All nuisance regression + linear detrending + scrubbing)
+          no_output_timeout: 8h
+          command: |
+            # Execute BIDS App
+            docker run -it --rm \
+            --entrypoint /app/run_coverage_cmp3.sh \
+            -v /tmp/data/${CIRCLE_JOB}/ds-sample:/bids_dir \
+            -v /tmp/data/${CIRCLE_JOB}/ds-sample/derivatives:/output_dir \
+            -v /home/circleci/src/connectomemapper3/.circleci/tests/configuration_files:/config \
+            sebastientourbier/connectomemapper3 \
+            /bids_dir /output_dir participant --participant_label 01 --session_label 01 \
+            --anat_pipeline_config /config/ref_anatomical_config_1.ini \
+            --func_pipeline_config /config/ref_fMRI_config_2.ini \
+            --fs_license /bids_dir/code/license.txt \
+            --coverage
+
+            # Rename partial coverage
+            mv /tmp/data/${CIRCLE_JOB}/ds-sample/code/coverage.xml /tmp/data/ds-sample/test/test-08_coverage.xml
+
+            # Rename execution log
+            mv /tmp/data/${CIRCLE_JOB}/ds-sample/code/log.txt /tmp/data/ds-sample/test/test-08_log.txt
+      - run:
+          name: Checking outputs of Connectome Mapper run (test 8)
+          command: |
+            # Get all files in derivatives except the _*.json interface hash generated by nipype (find) /
+            # Remove the full path of the derivatives (sed) / sort the files and write it to a text file
+            sudo find /tmp/data/${CIRCLE_JOB}/ds-sample/derivatives -path */figures -prune -o -not -name "_*.json" -type f -print | sed s+/tmp/data/${CIRCLE_JOB}/ds-sample/derivatives/++ | sort > /tmp/data/ds-sample/test/test-08_outputs.out
+            diff /home/circleci/src/connectomemapper3/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt /tmp/data/ds-sample/test/test-08_outputs.out
+            exit $?
       - persist_to_workspace:
           root: /tmp
           paths:
@@ -694,17 +754,35 @@ jobs:
   codacy_coverage_report:
     docker:
       - image: 'circleci/openjdk:8-jdk'
-
     working_directory: /tmp/data/ds-sample/code
-
     steps:
       - attach_workspace:
           at: /tmp
-      - coverage-reporter/send_report:
-          # With parcellation tests
-          coverage-reports: '/tmp/data/ds-sample/test/test-01_coverage.xml,/tmp/data/ds-sample/test/test-02_coverage.xml,/tmp/data/ds-sample/test/test-03_coverage.xml,/tmp/data/ds-sample/test/test-04_coverage.xml,/tmp/data/ds-sample/test/test-05_coverage.xml,/tmp/data/ds-sample/test/test-06_coverage.xml,/tmp/data/ds-sample/test/test-07_coverage.xml'
-          # coverage-reports: '/tmp/data/ds-sample/test/test-01_coverage.xml,/tmp/data/ds-sample/test/test-02_coverage.xml,/tmp/data/ds-sample/test/test-03_coverage.xml,/tmp/data/ds-sample/test/test-04_coverage.xml'
-          project-token: ${CODACY_PROJECT_TOKEN}
+      - run:
+          name: Run Codacy Coverage Reporter to convert and upload the reports to Codacy
+          command: |
+            export CODACY_REPORTER_VERSION=latest
+            export CODACY_PROJECT_TOKEN=${CODACY_PROJECT_TOKEN}
+            # Handles partial reports and send the final report to Codacy
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-01_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-02_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-03_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-04_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-05_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-06_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-07_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-08_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) report \
+                -l Python -r /tmp/data/ds-sample/test/test-09_coverage.xml --partial &&\
+            bash <(curl -Ls https://coverage.codacy.com/get.sh) final
 
   test_singularity_parcellation:
     machine:
@@ -1006,7 +1084,7 @@ jobs:
             # THISVERSION="$( python /home/circleci/src/connectomemapper3/get_version.py )"
             # echo "THISVERSION : ${THISVERSION}"
             echo "CIRCLE_TAG : ${CIRCLE_TAG}"
-            singularity push -U /tmp/cache/connectomemapper3.simg library://connectomicslab/default/connectomemapper-bidsapp:${CIRCLE_TAG}
+            singularity push -U /tmp/cache/connectomemapper3.simg library://connectomicslab/default/connectomemapper-bidsapp:latest
 
 workflows:
   version: 2.1
diff --git a/COPYRIGHT b/COPYRIGHT
index 8c85e2eaf..185da9060 100644
--- a/COPYRIGHT
+++ b/COPYRIGHT
@@ -1,4 +1,4 @@
-Copyright (C) 2009-2020, Ecole Polytechnique Fédérale de Lausanne (EPFL) and
+Copyright (C) 2009-2021, Ecole Polytechnique Fédérale de Lausanne (EPFL) and
 Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland & Contributors,
 All rights reserved.
 
diff --git a/DEVELOPER.rst b/DEVELOPER.rst
index ea47616e9..0da7dcb82 100644
--- a/DEVELOPER.rst
+++ b/DEVELOPER.rst
@@ -4,7 +4,8 @@ Connectome Mapper Developer Notes
 
 :Authors: Adrien Birbaumer and Sebastien Tourbier
 :Version: $Revision: 2 $
-:Copyright: Copyright (C) 2017-2019, Brain Communication Pathways Sinergia Consortium, Switzerland.
+:Copyright: Copyright (C) 2017-2021, Ecole Polytechnique Fédérale de Lausanne (EPFL) and
+            Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland & Contributors,
             This software is distributed under the open-source license Modified BSD.
 
 .. contents::
diff --git a/Dockerfile b/Dockerfile
index 47dc6eeaa..f8996cb97 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -169,9 +169,9 @@ RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/patches/fsl-5.0.10-python3.tar.
 # depend on it
 #RUN apt-mark manual package_name
 
-##################################################################
-## Install conda environment, including ANTs 2.2.0
-##################################################################
+###################################################################
+## Install conda environment, including ANTs 2.2.0 and MRtrix 3.0.2
+###################################################################
 FROM builder_afni as builder_conda_env
 
 WORKDIR /opt
@@ -186,66 +186,6 @@ RUN /bin/bash -c "conda env create -f /app/environment.yml && . activate $CONDA_
 ENV ANTSPATH="/opt/conda/envs/$CONDA_ENV/bin" \
     PATH="$ANTSPATH:$PATH"
 
-##################################################################
-## Install MRTRIX
-##################################################################
-FROM builder_conda_env as builder_mrtrix
-
-WORKDIR /opt
-
-# Additional dependencies for MRtrix3 compilation
-# Get the latest version of MRtrix3
-# MRtrix3 setup
-RUN apt-get update && \
-    apt-get install -y git && \
-    git clone https://github.com/MRtrix3/mrtrix3.git mrtrix3 && \
-    apt-get -y remove git && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-WORKDIR /opt/mrtrix3
-RUN apt-get update && \
-    apt-get install --no-install-recommends -y \
-    build-essential git g++ \
-    libeigen3-dev zlib1g-dev \
-    libfftw3-dev libtiff5-dev libssl-dev && \
-    git checkout -f 3.0_RC3_latest && \
-    python configure -nogui && \
-    python build -persistent -nopaginate && \
-    git describe --tags > /mrtrix3_version && \
-    apt-get -y remove build-essential git g++ && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-# Setup environment variables for MRtrix3
-ENV PATH="/opt/mrtrix3/bin:$PATH" \
-    PYTHONPATH="/opt/mrtrix3/lib:$PYTHONPATH"
-
-##################################################################
-## Install FSL 6.0.0
-##################################################################
-# FROM builder_mrtrix as builder_fsl
-
-# WORKDIR /opt
-# RUN apt-get update && \
-#     apt-get install -qq -y --no-install-recommends curl && \
-#     echo "Downloading FSL ..." \
-#     && curl -sSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
-#     | tar zx -C /opt \
-#     && /bin/bash /opt/fsl/etc/fslconf/fslpython_install.sh -q -f /opt/fsl \
-#     && rm -rf /opt/fsl/data/first \
-#     && rm -rf /opt/fsl/data/possum \
-#     && rm -rf /opt/fsl/data/atlases/HarvardOxford \
-#     && rm -rf /opt/fsl/data/atlases/JHU \
-#     && rm -rf /opt/fsl/data/atlases/Juelich \
-#     && rm -rf /opt/fsl/doc \
-#     && apt-get remove -y curl \
-#     && apt-get clean \
-#     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-# ENV FSLDIR=/opt/fsl \
-#     PATH=/opt/fsl/bin:$PATH
-
 ##################################################################
 # Install BIDS validator
 ##################################################################
@@ -260,7 +200,7 @@ ENV LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:/usr/lib:/usr/local/lib:$LD_LIBRARY_P
 ##################################################################
 # Installation of Connectome Mapper 3 packages
 ##################################################################
-FROM builder_mrtrix as builder_cmp3
+FROM builder_conda_env as builder_cmp3
 
 # Set the working directory to /app/connectomemapper3
 WORKDIR /app/connectomemapper3
@@ -271,14 +211,14 @@ COPY . /app/connectomemapper3
 # Install cmp and cmtklib packages in the conda environment $CONDA_ENV
 # ENV CONDA_ENV py37cmp-core
 # RUN apt-get -qq -y install libtiff5-dev=4.0.6-1ubuntu0.4 libssl-dev=1.0.2g-1ubuntu4.13
-RUN /bin/bash -c ". activate ${CONDA_ENV} && pip install networkx==2.4 &&\
-    python setup.py install && conda clean -v --all --yes && rm -rf ~/.conda ~/.cache/pip/*"
+RUN /bin/bash -c ". activate ${CONDA_ENV} &&\
+    python setup.py install"
 
 # Environmment setup
-ENV ANTSPATH="/opt/conda/envs/$CONDA_ENV/bin" \
-    PYTHONPATH="/opt/conda/envs/$CONDA_ENV/bin" \
+ENV ANTSPATH="/opt/conda/envs/${CONDA_ENV}/bin" \
+    PYTHONPATH="/opt/conda/envs/${CONDA_ENV}/bin" \
     PATH="$ANTSPATH:$PATH" \
-    LD_LIBRARY_PATH="/opt/conda/envs/$CONDA_ENV/lib:$LD_LIBRARY_PATH"
+    LD_LIBRARY_PATH="/opt/conda/envs/${CONDA_ENV}/lib:${LD_LIBRARY_PATH}"
 
 # Make dipy.viz (fury/vtk) happy
 # RUN /bin/bash -c "ln -s /opt/conda/envs/$CONDA_ENV/lib/libnetcdf.so.15 /opt/conda/envs/$CONDA_ENV/lib/libnetcdf.so.13"
@@ -335,8 +275,8 @@ ENV LANG="C.UTF-8" \
 # Unless otherwise specified each process should only use one
 # thread - nipype will handle parallelization
 ##################################################################
-# ENV MKL_NUM_THREADS=1 \
-#     OMP_NUM_THREADS=1
+ENV MKL_NUM_THREADS=1 \
+    OMP_NUM_THREADS=1
 
 ##################################################################
 # Control random number generation
@@ -378,11 +318,11 @@ ENTRYPOINT ["/app/run_cmp3.sh"]
 ##################################################################
 # Metadata
 ##################################################################
-LABEL org.label-schema.build-date=$BUILD_DATE \
+LABEL org.label-schema.build-date=${BUILD_DATE} \
       org.label-schema.name="Connectome Mapper BIDS App" \
       org.label-schema.description="Connectome Mapper BIDS App - the processing core of Connectome Mapper 3" \
       org.label-schema.url="https://connectome-mapper-3.readthedocs.io" \
-      org.label-schema.vcs-ref=$VCS_REF \
+      org.label-schema.vcs-ref=${VCS_REF} \
       org.label-schema.vcs-url="https://github.com/connectomicslab/connectomemapper3" \
       org.label-schema.version=$VERSION \
       org.label-schema.maintainer="Sebastien Tourbier <sebastien.tourbier@alumni.epfl.ch>" \
diff --git a/README.md b/README.md
index 02556df0f..8549ca823 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ This BIDS App has the following command line arguments:
               [--fs_license FS_LICENSE] [--coverage] [--notrack] [-v]
               bids_dir output_dir {participant,group}
 
-        Entrypoint script of the BIDS-App Connectome Mapper version v3.0.0-RC2
+        Entrypoint script of the BIDS-App Connectome Mapper version v3.0.0-RC3
 
         positional arguments:
           bids_dir              The directory with the input dataset formatted
@@ -85,8 +85,7 @@ This BIDS App has the following command line arguments:
                                 fMRI processing pipeline
           --number_of_threads NUMBER_OF_THREADS
                                 The number of OpenMP threads used for multi-threading
-                                by Freesurfer, FSL, MRtrix3, Dipy, AFNI (Set to
-                                [Number of available CPUs -1] by default).
+                                by Freesurfer (Set to [Number of available CPUs -1] by default).
           --number_of_participants_processed_in_parallel NUMBER_OF_PARTICIPANTS_PROCESSED_IN_PARALLEL
                                 The number of subjects to be processed in parallel
                                 (One by default).
diff --git a/cmp/bidsappmanager/gui.py b/cmp/bidsappmanager/gui.py
index 301bfdf2e..b40ba9e02 100644
--- a/cmp/bidsappmanager/gui.py
+++ b/cmp/bidsappmanager/gui.py
@@ -37,7 +37,7 @@
 from cmp.pipelines.diffusion.diffusion import DiffusionPipeline
 from cmp.pipelines.functional.fMRI import fMRIPipeline
 
-from cmtklib.util import return_button_style_sheet
+from cmtklib.util import return_button_style_sheet, BColors
 
 # Remove warnings visible whenever you import scipy (or another package) 
 # that was compiled against an older numpy than is installed.
@@ -1040,26 +1040,28 @@ def _start_bidsapp_fired(self):
 
     def check_settings(self):
         """Checks if all the parameters of the BIDS App run are properly set before execution."""
+        print('\n-----------------------------------------')
+        print('BIDS App execution settings check summary')
+        print('-----------------------------------------')
+
         self.settings_checked = True
 
         if os.path.isdir(self.bids_root):
-            print("BIDS root directory : {}".format(self.bids_root))
+            print(f'BIDS root directory : {self.bids_root}')
         else:
-            print("Error: BIDS root invalid!")
+            print(BColors.FAIL + "Error: BIDS root invalid!" + BColors.ENDC)
             self.settings_checked = False
 
         if os.path.exists(os.path.join(self.output_dir, 'cmp')):
-            print('Output directory (existing) : {}'.format(self.output_dir))
+            print(f'Output directory (existing) : {self.output_dir}')
         else:
             os.makedirs(os.path.join(self.output_dir, 'cmp'))
-            print('Output directory (created) : {}'.format(self.output_dir))
+            print(BColors.WARNING + f'Output directory (created) : {self.output_dir}' + BColors.ENDC)
 
         if len(self.list_of_subjects_to_be_processed) > 0:
-            print("Participant labels to be processed : {}".format(
-                self.list_of_subjects_to_be_processed))
+            print(f'Participant labels to be processed : {self.list_of_subjects_to_be_processed}')
         else:
-            print(
-                "Error: At least one participant label to be processed should selected!")
+            print(BColors.FAIL + "Error: At least one participant label to be processed should selected!" + BColors.ENDC)
             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))
@@ -1067,25 +1069,25 @@ def check_settings(self):
         #     print("Warning: List of subjects empty!")
 
         if os.path.isfile(self.anat_config):
-            print("Anatomical configuration file : {}".format(self.anat_config))
+            print(f'Anatomical configuration file : {self.anat_config}')
         else:
-            print("Error: Configuration file for anatomical pipeline not existing!")
+            print(BColors.FAIL + "Error: Configuration file for anatomical pipeline not existing!" + BColors.ENDC)
             self.settings_checked = False
 
         if os.path.isfile(self.dmri_config):
-            print("Diffusion configuration file : {}".format(self.dmri_config))
+            print(f'Diffusion configuration file : {self.dmri_config}')
         else:
-            print("Warning: Configuration file for diffusion pipeline not existing!")
+            print(BColors.WARNING + "Warning: Configuration file for diffusion pipeline not existing!" + BColors.ENDC)
 
         if os.path.isfile(self.fmri_config):
-            print("fMRI configuration file : {}".format(self.fmri_config))
+            print(f'fMRI configuration file : {self.fmri_config}')
         else:
-            print("Warning: Configuration file for fMRI pipeline not existing!")
+            print(BColors.WARNING + "Warning: Configuration file for fMRI pipeline not existing!" + BColors.ENDC)
 
         if os.path.isfile(self.fs_license):
-            print("Freesurfer license : {}".format(self.fs_license))
+            print(f'Freesurfer license : {self.fs_license}')
         else:
-            print("Error: Invalid Freesurfer license ({})!".format(self.fs_license))
+            print(BColors.FAIL + f'Error: Invalid Freesurfer license ({self.fs_license})!' + BColors.ENDC)
             self.settings_checked = False
 
         # if os.path.isdir(self.fs_average):
@@ -1094,15 +1096,26 @@ def check_settings(self):
         #     print("Error: fsaverage directory ({}) not existing!".format(self.fs_average))
         #     self.settings_checked = False
 
-        print("Valid inputs for BIDS App : {}".format(self.settings_checked))
-        print("BIDS App Version Tag: {}".format(self.bidsapp_tag))
-        print("Data provenance tracking (datalad) : {}".format(
-            self.data_provenance_tracking))
-        print("Update computing environment (datalad) : {}".format(
-            self.datalad_update_environment))
-        print("Number of participant processed in parallel : {}".format(
-            self.number_of_participants_processed_in_parallel))
-        print("Number of threads / participant : {}".format(self.number_of_threads))
+        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'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'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}')
+        if self.fix_ants_random_seed:
+            print(f'Seed value : {self.mrtrix_random_seed}')
+
+        print('-----------------------------------------\n')
 
         return True
 
diff --git a/cmp/info.py b/cmp/info.py
index 9c7d2c54a..31ffb9d47 100644
--- a/cmp/info.py
+++ b/cmp/info.py
@@ -3,7 +3,7 @@
 _version_major = 3
 _version_minor = 0
 _version_micro = 0
-_version_extra = '-RC2'
+_version_extra = '-RC3'
 __release_date__ = '24.12.2020'
 
 __minor_version__ = "%s.%s" % (_version_major,
diff --git a/cmp/parser.py b/cmp/parser.py
index 6dd708c73..67fbb0ae1 100644
--- a/cmp/parser.py
+++ b/cmp/parser.py
@@ -58,8 +58,7 @@ def get():
     p.add_argument('--number_of_threads',
                    type=int,
                    help='The number of OpenMP threads used for multi-threading by '
-                        'Freesurfer, FSL, MRtrix3, Dipy, AFNI '
-                        '(Set to [Number of available CPUs -1] by default).')
+                        'Freesurfer (Set to [Number of available CPUs -1] by default).')
 
     p.add_argument('--number_of_participants_processed_in_parallel',
                    default=1,
diff --git a/cmp/project.py b/cmp/project.py
index 3205510be..edec7eb22 100644
--- a/cmp/project.py
+++ b/cmp/project.py
@@ -1,5 +1,5 @@
-# Copyright (C) 2009-2019, Ecole Polytechnique Federale de Lausanne (EPFL) and
-# Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland
+# Copyright (C) 2009-2021, 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.
diff --git a/cmp/stages/preprocessing/preprocessing.py b/cmp/stages/preprocessing/preprocessing.py
index bc38ffa8c..32a13e1aa 100644
--- a/cmp/stages/preprocessing/preprocessing.py
+++ b/cmp/stages/preprocessing/preprocessing.py
@@ -428,7 +428,7 @@ def convertList2Tuple(lists):
                         use_fsl=True, out_bias='diffusion_denoised_biasfield.mif'),
                     name='dwi_biascorrect')
 
-            dwi_biascorrect.inputs.debug = True
+            dwi_biascorrect.inputs.debug = False
 
             if self.config.denoising:
                 if self.config.denoising_algo == "MRtrix (MP-PCA)":
@@ -437,8 +437,8 @@ def convertList2Tuple(lists):
                          [('out_file', 'in_file')]),
                         (flirt_dwimask, dwi_biascorrect,
                          [('out_file', 'mask')]),
-                        (dwi_biascorrect, mr_convert_b,
-                         [('out_file', 'in_file')])
+                        # (dwi_biascorrect, mr_convert_b,
+                        #  [('out_file', 'in_file')])
                     ])
                 elif self.config.denoising_algo == "Dipy (NLM)":
                     flow.connect([
@@ -446,8 +446,8 @@ def convertList2Tuple(lists):
                          [('converted', 'in_file')]),
                         (flirt_dwimask, dwi_biascorrect,
                          [('out_file', 'mask')]),
-                        (dwi_biascorrect, mr_convert_b,
-                         [('out_file', 'in_file')])
+                        # (dwi_biascorrect, mr_convert_b,
+                        #  [('out_file', 'in_file')])
                     ])
             else:
                 flow.connect([
@@ -456,6 +456,7 @@ def convertList2Tuple(lists):
                 ])
 
             flow.connect([
+                (dwi_biascorrect, mr_convert_b, [('out_file', 'in_file')]),
                 (dwi_biascorrect, mr_convert_bias, [('out_file', 'in_file')]),
                 (mr_convert_bias, outputnode, [('converted', 'diffusion_biasfield')])
             ])
diff --git a/cmtklib/interfaces/dipy.py b/cmtklib/interfaces/dipy.py
index 1f05f6439..1fbb605c8 100644
--- a/cmtklib/interfaces/dipy.py
+++ b/cmtklib/interfaces/dipy.py
@@ -223,7 +223,7 @@ class CSD(DipyDiffusionInterface):
     output_spec = CSDOutputSpec
 
     def _run_interface(self, runtime):
-        from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel, auto_response
+        from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel, auto_response_ssst
         from dipy.data import get_sphere
         # import marshal as pickle
         import pickle as pickle
@@ -265,19 +265,23 @@ def clipMask(mask):
                 IFLOGGER.warn(('Estimated response is not prolate enough. '
                                'Ratio=%0.3f.') % ratio)
         else:
-            response, ratio, counts = auto_response(
-                gtab, data, fa_thr=0.5, return_number_of_voxels=True)
+            response, ratio = auto_response_ssst(gtab,
+                                                         data,
+                                                         roi_radii=10,
+                                                         fa_thr=0.5)
             IFLOGGER.info("response: ")
             IFLOGGER.info(response)
             IFLOGGER.info("ratio: %g" % ratio)
-            IFLOGGER.info("nbr_voxel_used: %g" % counts)
 
             if abs(ratio - 0.2) > 0.1:
                 IFLOGGER.warn(('Estimated response is not prolate enough. '
                                'Ratio=%0.3f.') % ratio)
 
         sphere = get_sphere('symmetric724')
-        csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=self.inputs.sh_order, reg_sphere=sphere,
+        csd_model = ConstrainedSphericalDeconvModel(gtab,
+                                                    response,
+                                                    sh_order=self.inputs.sh_order,
+                                                    reg_sphere=sphere,
                                                     lambda_=np.sqrt(1. / 2))
         # IFLOGGER.info('Fitting CSD model')
         # csd_fit = csd_model.fit(data, msk)
@@ -311,8 +315,7 @@ def clipMask(mask):
             # IFLOGGER.info(fods)
             # IFLOGGER.info(fods.shape)
             IFLOGGER.info('Save Spherical Harmonics image')
-            nib.Nifti1Image(csd_peaks.shm_coeffs, img.affine, None).to_filename(
-                self._gen_filename('shm_coeff'))
+            nib.Nifti1Image(csd_peaks.shm_coeff, img.affine, None).to_filename(self._gen_filename('shm_coeff'))
 
             # FIXME: dipy 1.1.0 and fury 0.5.1 with vtk 8.2.0 -> error:
             #
@@ -559,9 +562,11 @@ class TensorInformedEudXTractography(DipyBaseInterface):
     def _run_interface(self, runtime):
         from dipy.tracking import utils
         from dipy.direction import peaks_from_model
-        # from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion, BinaryStoppingCriterion
-        from dipy.tracking.eudx import EuDX  # FIXME: see changes in Dipy 1.0
+        # from dipy.tracking.stopping_criterion import BinaryStoppingCriterion
+        from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion
+        from dipy.tracking.local_tracking import LocalTracking
         from dipy.data import get_sphere
+        from dipy.io.stateful_tractogram import Space, StatefulTractogram
         from dipy.io.streamline import save_trk
         # import marshal as pickle
         import pickle as pickle
@@ -584,7 +589,7 @@ def _run_interface(self, runtime):
         trkhdr['voxel_order'] = 'ras'
         # trackvis_affine = utils.affine_for_trackvis(trkhdr['voxel_size'])
 
-        sphere = get_sphere('repulsion724')
+        sphere = get_sphere('symmetric724')
 
         def clipMask(mask):
             """This is a hack until we fix the behaviour of the tracking objects around the edge of the image."""
@@ -608,29 +613,33 @@ def clipMask(mask):
 
         if isdefined(self.inputs.seed_mask[0]):
             IFLOGGER.info('Loading Seed Mask')
-            seedmsk = clipMask(nib.load(self.inputs.seed_mask[0]).get_data())
+            seedmsk = nib.load(self.inputs.seed_mask[0]).get_data()
+            IFLOGGER.info(f'  - Loaded Seed Mask Shape: {seedmsk.shape}')
+            # seedmsk = clipMask(nib.load(self.inputs.seed_mask[0]).get_data())
             # assert (seedmsk.shape == data.shape[:3])
             seedmsk[seedmsk > 0] = 1
             seedmsk[seedmsk < 1] = 0
             seedps = np.array(np.where(seedmsk == 1), dtype=np.float32).T
             vseeds = seedps.shape[0]
             nsperv = (seeds // vseeds) + 1
-            IFLOGGER.info(('Seed mask is provided (%d voxels inside '
-                           'mask), computing seeds (%d seeds/voxel).') %
-                          (vseeds, nsperv))
+            IFLOGGER.info(f'Seed mask is provided ({vseeds} voxels inside '
+                          f'mask), computing seeds ({nsperv} seeds/voxel).')
             if nsperv > 1:
-                IFLOGGER.info(('Needed %d seeds per selected voxel '
-                               '(total %d).') % (nsperv, vseeds))
+                IFLOGGER.info(f'Needed {nsperv} seeds per selected voxel (total {vseeds}).')
                 seedps = np.vstack(np.array([seedps] * nsperv))
                 voxcoord = seedps + np.random.uniform(-1, 1, size=seedps.shape)
                 nseeds = voxcoord.shape[0]
-                seeds = affine.dot(np.vstack((voxcoord.T,
-                                              np.ones((1, nseeds)))))[:3, :].T
+                seeds = affine.dot(np.vstack((voxcoord.T, np.ones((1, nseeds)))))[:3, :].T
 
                 if self.inputs.save_seeds:
                     np.savetxt(self._gen_filename('seeds', ext='.txt'), seeds)
 
-            # tseeds = utils.seeds_from_mask(seedmsk, density=2, affine=affine)
+            IFLOGGER.info(f'Create seeds for fiber tracking from the binary seed mask (density: {nsperv})')
+
+            tseeds = utils.seeds_from_mask(seedmsk,
+                                           affine=affine,
+                                           density=[nsperv, nsperv, nsperv]  # FIXME: density should be customizable
+                                           )
 
         IFLOGGER.info('Loading and masking FA')
         img_fa = nib.load(self.inputs.in_fa)
@@ -643,7 +652,7 @@ def clipMask(mask):
             self._gen_filename('fa_masked'))
 
         IFLOGGER.info('Building Tissue Classifier')
-        # classifier = ThresholdStoppingCriterion(fa,self.inputs.fa_thresh)
+        classifier = ThresholdStoppingCriterion(fa, self.inputs.fa_thresh)
         # classifier = BinaryStoppingCriterion(tmsk)
 
         IFLOGGER.info('Loading tensor model')
@@ -652,50 +661,26 @@ def clipMask(mask):
         f.close()
 
         IFLOGGER.info('Generating peaks from tensor model')
-        pfm = peaks_from_model(model=tensor_model,
-                               data=data,
-                               sphere=sphere,
-                               relative_peak_threshold=.2,
-                               min_separation_angle=25,
-                               mask=tmsk,
-                               return_sh=True,
-                               # sh_basis_type=args.basis,
-                               sh_order=8,
-                               normalize_peaks=False,  # changed
-                               parallel=True)
+        dti_peaks = peaks_from_model(model=tensor_model,
+                                     data=data,
+                                     sphere=sphere,
+                                     relative_peak_threshold=.2,
+                                     min_separation_angle=25,
+                                     mask=tmsk,
+                                     normalize_peaks=False,  # changed
+                                     parallel=True)
 
         IFLOGGER.info('Performing tensor-informed EuDX tractography')
-
-        streamlines = EuDX(pfm.peak_values,
-                           pfm.peak_indices,
-                           seeds=seeds,
-                           affine=affine,
-                           odf_vertices=sphere.vertices,
-                           step_sz=self.inputs.step_size,
-                           a_low=self.inputs.fa_thresh)
+        streamlines = LocalTracking(dti_peaks,
+                                    classifier,
+                                    tseeds,
+                                    affine,
+                                    step_size=self.inputs.step_size,
+                                    max_cross=1)
 
         IFLOGGER.info('Saving tracks')
-        save_trk(self._gen_filename('tracked', ext='.trk'),
-                 streamlines, affine, fa.shape)
-
-        # IFLOGGER.info('Loading CSD model and fitting')
-        # f = gzip.open(self.inputs.in_model, 'rb')
-        # csd_model = pickle.load(f)
-        # f.close()
-
-        # csd_fit = csd_model.fit(data, mask=tmsk)
-
-        # if self.inputs.algo == 'deterministic':
-        #     dg = DeterministicMaximumDirectionGetter.from_shcoeff(csd_fit.shm_coeff, max_angle=self.inputs.max_angle, sphere=sphere)
-        # else:
-        #     dg = ProbabilisticDirectionGetter.from_shcoeff(csd_fit.shm_coeff, max_angle=self.inputs.max_angle, sphere=sphere)
-
-        # IFLOGGER.info(('Performing %s tractography') % (self.inputs.algo))
-
-        # streamlines = LocalTracking(dg, classifier, tseeds, affine, step_size=self.inputs.step_size)
-
-        # IFLOGGER.info('Saving tracks')
-        # save_trk(self._gen_filename('tracked', ext='.trk'), streamlines, affine, fa.shape)
+        sft = StatefulTractogram(streamlines, imref, Space.RASMM)
+        save_trk(sft, self._gen_filename('tracked', ext='.trk'))
 
         return runtime
 
@@ -725,44 +710,57 @@ def _gen_filename(self, name, ext=None):
 
 
 class DirectionGetterTractographyInputSpec(BaseInterfaceInputSpec):
-    algo = traits.Enum(["deterministic", "probabilistic"], usedefault=True,
-                       desc=(
-                           'Use either deterministic maximum (default) or probabilistic direction getter tractography'))
-    recon_model = traits.Enum(["CSD", "SHORE"], usedefault=True,
+    algo = traits.Enum(["deterministic", "probabilistic"],
+                       usedefault=True,
+                       desc='Use either deterministic maximum (default) or probabilistic direction getter tractography')
+    recon_model = traits.Enum(["CSD", "SHORE"],
+                              usedefault=True,
                               desc='Use either fODFs from CSD (default) or SHORE models')
-    recon_order = traits.Int(8)
-    use_act = traits.Bool(False, desc=(
-        'Use FAST for partial volume estimation and Anatomically-Constrained Tractography (ACT) tissue classifier'))
-    seed_from_gmwmi = traits.Bool(False, desc=(
-        'Seed from the Gray Matter / White Matter interface'))
-    gmwmi_file = File(exists=True, desc=(
-        'input Gray Matter / White Matter interface image'))
+    recon_order = traits.Int(8,
+                             desc='Spherical harmonics order')
+    use_act = traits.Bool(False,
+                          desc='Use FAST for partial volume estimation and '
+                               'Anatomically-Constrained Tractography (ACT) tissue classifier')
+    seed_from_gmwmi = traits.Bool(False,
+                                  desc='Seed from the Gray Matter / White Matter interface')
+    gmwmi_file = File(exists=True,
+                      desc='input Gray Matter / White Matter interface image')
     # fast_number_of_classes = traits.Int(3, desc=('Number of tissue classes used by FAST for Anatomically-Constrained Tractography (ACT)'))
-    in_file = File(exists=True, mandatory=True, desc='input diffusion data')
-    fod_file = File(exists=True, desc='input fod file (if SHORE)')
-    in_fa = File(exists=True, mandatory=True, desc='input FA')
+    in_file = File(exists=True, mandatory=True,
+                   desc='input diffusion data')
+    fod_file = File(exists=True,
+                    desc='input fod file (if SHORE)')
+    in_fa = File(exists=True, mandatory=True,
+                 desc='input FA')
     in_partial_volume_files = InputMultiPath(File(exists=True),
                                              desc='Partial volume estimation result files (required if performing ACT)')
     # in_t1 = File(exists=True, desc=('input T1w (required if performing ACT)'))
-    in_model = File(exists=True, mandatory=True, desc=(
-        'input f/d-ODF model extracted from.'))
+    in_model = File(exists=True, mandatory=True,
+                    desc='input f/d-ODF model extracted from.')
     tracking_mask = File(exists=True, mandatory=True,
                          desc='input mask within which perform tracking')
-    seed_mask = InputMultiPath(File(
-        exists=True), mandatory=True, desc='ROI files registered to diffusion space')
-    seed_density = traits.Float(1, usedefault=True,
+    seed_mask = InputMultiPath(File(exists=True), mandatory=True,
+                               desc='ROI files registered to diffusion space')
+    seed_density = traits.Float(1,
+                                usedefault=True,
                                 desc='Density of seeds')
-    fa_thresh = traits.Float(0.2, mandatory=True, usedefault=True,
+    fa_thresh = traits.Float(0.2,
+                             mandatory=True, usedefault=True,
                              desc='FA threshold to build the tissue classifier')
-    max_angle = traits.Float(25.0, mandatory=True, usedefault=True,
+    max_angle = traits.Float(25.0,
+                             mandatory=True, usedefault=True,
                              desc='Maximum angle')
-    step_size = traits.Float(0.5, mandatory=True, usedefault=True,
+    step_size = traits.Float(0.5,
+                             mandatory=True, usedefault=True,
                              desc='Step size')
-    multiprocess = traits.Bool(True, mandatory=True, usedefault=True,
+    multiprocess = traits.Bool(True,
+                               mandatory=True, usedefault=True,
                                desc='use multiprocessing')
-    save_seeds = traits.Bool(False, mandatory=True, usedefault=True,
+    save_seeds = traits.Bool(False,
+                             mandatory=True, usedefault=True,
                              desc='save seeding voxels coordinates')
-    num_seeds = traits.Int(10000, mandatory=True, usedefault=True,
+    num_seeds = traits.Int(10000,
+                           mandatory=True, usedefault=True,
                            desc='desired number of tracks in tractography')
     out_prefix = traits.Str(desc='output prefix for file names')
 
@@ -794,16 +792,15 @@ class DirectionGetterTractography(DipyBaseInterface):
 
     def _run_interface(self, runtime):
         from dipy.tracking import utils
-        from dipy.direction import DeterministicMaximumDirectionGetter, \
-            ProbabilisticDirectionGetter
+        from dipy.direction import DeterministicMaximumDirectionGetter, ProbabilisticDirectionGetter
         # from dipy.tracking.local import ThresholdStoppingCriterion, ActStoppingCriterion
         from dipy.tracking.stopping_criterion import BinaryStoppingCriterion, CmcStoppingCriterion
         from dipy.tracking.local_tracking import LocalTracking, ParticleFilteringTracking
         from dipy.direction.peaks import peaks_from_model
         from dipy.data import get_sphere
+        from dipy.tracking.streamline import Streamlines
         from dipy.io.stateful_tractogram import Space, StatefulTractogram
         from dipy.io.streamline import save_trk
-        # import marshal as pickle
         import pickle
         import gzip
 
@@ -822,7 +819,7 @@ def _run_interface(self, runtime):
         sphere = get_sphere('symmetric724')
 
         def clipMask(mask):
-            """This is a hack until we fix the behaviour of the tracking objects
+            """This is a hack until Dipy fixes the behaviour of the tracking objects
             around the edge of the image"""
             out = mask.copy()
             index = [slice(None)] * out.ndim
@@ -919,49 +916,51 @@ def clipMask(mask):
 
             # Handle GMWM interface or seed mask
             if self.inputs.seed_from_gmwmi and isdefined(self.inputs.gmwmi_file):
-                IFLOGGER.info('Loading Seed Mask from {}'.format(
-                    self.inputs.gmwmi_file))
+                IFLOGGER.info(f'Loading Seed Mask from {self.inputs.gmwmi_file}')
                 seedmsk = nib.load(self.inputs.gmwmi_file).get_data()
                 seedmsk = np.squeeze(seedmsk)
             else:
-                IFLOGGER.info('Loading Seed Mask from {}'.format(
-                    self.inputs.seed_mask[0]))
+                IFLOGGER.info(f'Loading Seed Mask from {self.inputs.seed_mask[0]}')
                 seedmsk = nib.load(self.inputs.seed_mask[0]).get_data()
 
             # assert (seedmsk.shape == data.shape[:3])
-            seedmsk = clipMask(seedmsk)
+            # seedmsk = clipMask(seedmsk)
 
-            print('seedmsk min: {}'.format(seedmsk.min()))
-            print('seedmsk max: {}'.format(seedmsk.max()))
+            print(f'seedmsk min: {seedmsk.min()}')
+            print(f'seedmsk max: {seedmsk.max()}')
 
             seedmsk[seedmsk > 0] = 1
             seedmsk[seedmsk < 1] = 0
 
-            IFLOGGER.info('Saving seed mask')
+            IFLOGGER.info(f'Saving seed mask (shape: {seedmsk.shape})')
             hdr.set_data_shape(seedmsk.shape)
-            nib.Nifti1Image(seedmsk.astype(np.float32), affine, hdr).to_filename(
-                self._gen_filename('desc-seed_mask'))
+            nib.Nifti1Image(seedmsk.astype(np.float32),
+                            affine,
+                            hdr).to_filename(self._gen_filename('desc-seed_mask'))
 
             seedps = np.array(np.where(seedmsk == 1), dtype=np.float32).T
             vseeds = seedps.shape[0]
             nsperv = (seeds // vseeds) + 1
-            IFLOGGER.info(('Seed mask is provided (%d voxels inside '
-                           'mask), computing seeds (%d seeds/voxel).') %
-                          (vseeds, nsperv))
+            IFLOGGER.info(f'Seed mask is provided ({vseeds} voxels inside '
+                          f'mask), computing seeds ({nsperv} seeds/voxel).')
             if nsperv > 1:
-                IFLOGGER.info(('Needed %d seeds per selected voxel '
-                               '(total %d).') % (nsperv, vseeds))
+                IFLOGGER.info(f'Needed {nsperv} seeds per selected voxel '
+                              f'(total {vseeds}).')
                 seedps = np.vstack(np.array([seedps] * nsperv))
                 voxcoord = seedps + np.random.uniform(-1, 1, size=seedps.shape)
                 nseeds = voxcoord.shape[0]
-                seeds = affine.dot(np.vstack((voxcoord.T,
-                                              np.ones((1, nseeds)))))[:3, :].T
+                seeds = affine.dot(np.vstack((voxcoord.T, np.ones((1, nseeds)))))[:3, :].T
 
                 if self.inputs.save_seeds:
                     np.savetxt(self._gen_filename('seeds', ext='.txt'), seeds)
 
-            tseeds = utils.seeds_from_mask(seedmsk, density=self.inputs.seed_density,
-                                           affine=affine)  # FIXME: density should be customizable
+            IFLOGGER.info(f'Create seeds for fiber tracking from the binary seed mask (density: {self.inputs.seed_density})')
+            tseeds = utils.seeds_from_mask(seedmsk,
+                                           affine=affine,
+                                           density=[self.inputs.seed_density,
+                                                    self.inputs.seed_density,
+                                                    self.inputs.seed_density]  # FIXME: density should be customizable
+                                           )
 
         if self.inputs.recon_model == 'CSD':
             IFLOGGER.info('Loading CSD model')
@@ -983,36 +982,40 @@ def clipMask(mask):
                                    parallel=True)
 
             if self.inputs.algo == 'deterministic':
-                dg = DeterministicMaximumDirectionGetter.from_shcoeff(pfm.shm_coeffs, max_angle=self.inputs.max_angle,
+                dg = DeterministicMaximumDirectionGetter.from_shcoeff(pfm.shm_coeff,
+                                                                      max_angle=self.inputs.max_angle,
                                                                       sphere=sphere)
             else:
-                dg = ProbabilisticDirectionGetter.from_shcoeff(pfm.shm_coeffs, max_angle=self.inputs.max_angle,
+                dg = ProbabilisticDirectionGetter.from_shcoeff(pfm.shm_coeff,
+                                                               max_angle=self.inputs.max_angle,
                                                                sphere=sphere)
-
         else:
-
             IFLOGGER.info('Loading SHORE FOD')
             sh = nib.load(self.inputs.fod_file).get_data()
             sh = np.nan_to_num(sh)
             IFLOGGER.info('Generating peaks from SHORE model')
             if self.inputs.algo == 'deterministic':
-                dg = DeterministicMaximumDirectionGetter.from_shcoeff(sh, max_angle=self.inputs.max_angle,
+                dg = DeterministicMaximumDirectionGetter.from_shcoeff(sh,
+                                                                      max_angle=self.inputs.max_angle,
                                                                       sphere=sphere)
             else:
-                dg = ProbabilisticDirectionGetter.from_shcoeff(
-                    sh, max_angle=self.inputs.max_angle, sphere=sphere)
+                dg = ProbabilisticDirectionGetter.from_shcoeff(sh,
+                                                               max_angle=self.inputs.max_angle,
+                                                               sphere=sphere)
 
         if not self.inputs.use_act:
-
             IFLOGGER.info('Performing %s tractography' % self.inputs.algo)
 
-            streamlines = LocalTracking(
-                dg, classifier, tseeds, affine, step_size=self.inputs.step_size, max_cross=1)
+            streamlines = LocalTracking(dg,
+                                        classifier,
+                                        tseeds,
+                                        affine,
+                                        step_size=self.inputs.step_size,
+                                        max_cross=1)
 
             IFLOGGER.info('Saving tracks')
             sft = StatefulTractogram(streamlines, imref, Space.RASMM)
             save_trk(sft, self._gen_filename('tracked', ext='.trk'))
-
         else:
             IFLOGGER.info('Performing PFT tractography')
             # Particle Filtering Tractography
@@ -1027,12 +1030,8 @@ def clipMask(mask):
                                                                  pft_front_tracking_dist=1,
                                                                  particle_count=15,
                                                                  return_all=False)
-
-            # streamlines = list(pft_streamline_generator)
-
             IFLOGGER.info('Saving tracks')
-            from dipy.tracking.streamline import Streamlines
-
+            # streamlines = list(pft_streamline_generator)
             streamlines = Streamlines(pft_streamline_generator)
             sft = StatefulTractogram(streamlines, imref, Space.RASMM)
             save_trk(sft, self._gen_filename('tracked', ext='.trk'))
diff --git a/cmtklib/interfaces/mrtrix3.py b/cmtklib/interfaces/mrtrix3.py
index 0634a5b74..469e2eb61 100644
--- a/cmtklib/interfaces/mrtrix3.py
+++ b/cmtklib/interfaces/mrtrix3.py
@@ -247,8 +247,8 @@ def _gen_filename(self, name):
 
 
 class DWIBiasCorrectInputSpec(CommandLineInputSpec):
-    in_file = File(exists=True, argstr='%s', mandatory=True,
-                   position=-2, desc='The input image series to be corrected')
+    in_file = File(exists=True, argstr='%s', mandatory=True, position=-2,
+                   desc='The input image series to be corrected')
 
     out_file = File(genfile=True, argstr='%s', position=-1,
                     desc='The output corrected image series')
@@ -261,14 +261,14 @@ class DWIBiasCorrectInputSpec(CommandLineInputSpec):
 
     _xor_inputs = ('use_ants', 'use_fsl')
 
-    use_ants = traits.Bool(argstr='-ants', position=1, desc="Use ANTS N4 to estimate the inhomogeneity field",
+    use_ants = traits.Bool(argstr='ants', position=1, desc="Use ANTS N4 to estimate the inhomogeneity field",
                            xor=_xor_inputs)
 
-    use_fsl = traits.Bool(argstr='-fsl', position=1, desc="Use FSL FAST to estimate the inhomogeneity field",
+    use_fsl = traits.Bool(argstr='fsl', position=1, desc="Use FSL FAST to estimate the inhomogeneity field",
                           xor=_xor_inputs)
 
-    force_writing = traits.Bool(
-        argstr='-force', position=4, desc="Force file overwriting.")
+    force_writing = traits.Bool(argstr='-force', position=4,
+                                desc="Force file overwriting.")
     # quiet = traits.Bool(argstr='-quiet', position=1, desc="Do not display information messages or progress status.")
 
     debug = traits.Bool(argstr='-debug', position=5,
@@ -302,8 +302,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
         """Generate a filename based on the given parameters.
 
         The filename will take the form: cwd/basename<suffix><ext>.
-        If change_ext is True, it will use the extentions specified in
-        <instance>intputs.output_type.
+        If change_ext is True, it will use the extensions specified in
+        <instance> inputs.output_type.
 
         Parameters
         ----------
diff --git a/docs/LICENSE.rst b/docs/LICENSE.rst
index 07e517c47..6044541da 100644
--- a/docs/LICENSE.rst
+++ b/docs/LICENSE.rst
@@ -3,7 +3,7 @@
 BSD 3-Clause License
 =======================================================
 
-Copyright (C) 2009-2020, Ecole Polytechnique Fédérale de Lausanne (EPFL) and
+Copyright (C) 2009-2021, Ecole Polytechnique Fédérale de Lausanne (EPFL) and
 Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland, & Contributors,
 All rights reserved.
 
diff --git a/docs/bidsappmanager.rst b/docs/bidsappmanager.rst
index 61c00ca3d..739c57a58 100644
--- a/docs/bidsappmanager.rst
+++ b/docs/bidsappmanager.rst
@@ -10,22 +10,20 @@ Introduction
 Connectome Mapper 3 comes with a Graphical User Interface, the Connectome Mapper BIDS App manager, designed to facilitate the configuration of all pipeline stages, the configuration of the BIDS App run and its execution, and the inspection of the different stage outputs with appropriate viewers.
 
 .. figure:: images/mainWindow.png
-	:align: center
-
-	Main window of the Connectome Mapper BIDS App Manager
-
+    :align: center
 
+    Main window of the Connectome Mapper BIDS App Manager
 
 Start the Graphical User Interface
 ***************************************
 
 In a terminal, enter to following::
 
-    $ source activate py27cmp-gui
+    $ source activate py37cmp-gui
 
 or::
 
-    $ conda activate py27cmp-gui
+    $ conda activate py37cmp-gui
 
 Please see Section :ref:`manual-install-cmpbidsappmanager` for more details about installation.
 
@@ -39,7 +37,7 @@ Load a BIDS dataset
 
 The ``Connectome Mapper 3`` BIDS App Manager allows you to:
 
-* load a BIDS dataset stored locally
+* load a BIDS dataset stored locally.
 
 You only have to select the root directory of your valid BIDS dataset (see note below)
 
@@ -51,7 +49,6 @@ If ssh connection is used, make sure to enable the  "install via ssh" and to pro
 
 .. note:: The input dataset MUST be a valid :abbr:`BIDS (Brain Imaging Data Structure)` structured dataset and must include at least one T1w or MPRAGE structural image. We highly recommend that you validate your dataset with the free, online `BIDS Validator <http://bids-standard.github.io/bids-validator/>`_.
 
-
 Pipeline stage configuration
 *****************************
 
@@ -61,14 +58,14 @@ Start the Configurator Window
 * From the main window, click on the left button to start the Configurator Window.
 
 .. image:: images/mainWindow_configurator.png
-	:align: center
+    :align: center
 
 * The window of the Connectome Mapper BIDS App Configurator will appear, which will assist you note only in configuring the pipeline stages (each pipeline has a tab panel), but also in creating appropriate configuration files which could be used outside the Graphical User Interface.
 
 .. figure:: images/configurator_window.png
-	:align: center
+    :align: center
 
-	Configurator Window of the Connectome Mapper
+    Configurator Window of the Connectome Mapper
 
 The outputs depend on the chosen parameters.
 
@@ -76,77 +73,61 @@ Anatomical pipeline stages
 ---------------------------
 
 .. figure:: images/configurator_pipeline_anat.png
-	:align: center
-
-	Panel for configuration of anatomical pipeline stages
+    :align: center
 
+    Panel for configuration of anatomical pipeline stages
 
 Segmentation
 """"""""""""""
 
-Performs tissue segmentation using Freesurfer or custom segmentation.
+Performs tissue segmentation using Freesurfer.
 
 *Freesurfer*
 
- 	.. image:: images/segmentation_fs.png
-		:align: center
-
-	* *Freesurfer args:* used to specify Freesurfer processing options
-	* *Use existing freesurfer data:* Check this box if you have already Freesurfer output data available
+    .. image:: images/segmentation_fs.png
+        :align: center
 
-*Custom segmentation*
+    * *Number of threads:* used to specify how many threads are used for parallelization
+    * *Brain extraction tools:* alternative brain extraction methods injected in Freesurfer
+    * *Freesurfer args:* used to specify extra Freesurfer processing options
 
-	.. warning:: Not fully tested. Development and testing in progress.
-
- 	.. image:: images/segmentation_custom.png
-		:align: center
-
-	* *White matter mask:* select the file containing your white matter binary mask
+    .. note:: If you have already Freesurfer output data available, CMP3 can use them if there are placed in your output / derivatives directory.
 
 Parcellation
 """"""""""""""
 
-Generates the Native Freesurfer or Lausanne2008/Lausanne2018 parcellation from Freesurfer data, or takes a custom parcellation atlas.
+Generates the Native Freesurfer or Lausanne2008/Lausanne2018 parcellation from Freesurfer data.
 
 **Parcellation scheme**
 
-	* *NativeFreesurfer:*
-
-		.. image:: images/parcellation_fs.png
-			:align: center
-
-		Atlas composed of 83 regions from the Freesurfer aparc+aseg file
-
-	* *Lausanne2008:*
+    * *NativeFreesurfer:*
 
-		.. image:: images/parcellation_lausanne2008.png
-			:align: center
+        .. image:: images/parcellation_fs.png
+            :align: center
 
-		Multi-resolution atlas
+        Atlas composed of 83 regions from the Freesurfer aparc+aseg file
 
-	* *Lausanne2018:*
+    * *Lausanne2008:*
 
-		.. image:: images/parcellation_lausanne2018.png
-			:align: center
+        .. image:: images/parcellation_lausanne2008.png
+            :align: center
 
-		Lausanne 2008 atlas extended with 7 thalamic nuclei, 12 hippocampal subfields, and 4 brainstem sub-structure per hemisphere
+        Multi-resolution atlas
 
-	* *Custom:*
+    * *Lausanne2018:*
 
-		.. warning:: Not fully tested. Development and testing in progress.
+        .. image:: images/parcellation_lausanne2018.png
+            :align: center
 
-		.. image:: images/parcellation_custom.png
-			:align: center
-
-		Custom atlas. Specify the atlas name, the number of regions, the nifti file and a corresponding graphml file. The Graphml file must contain at least a "dn_correspondence_id" field for each node. This field should contain the region's label in the nifti file.
+        Lausanne 2008 atlas extended with 7 thalamic nuclei, 12 hippocampal subfields, and 4 brainstem sub-structure per hemisphere
 
 Diffusion pipeline stages
 ---------------------------
 
 .. figure:: images/configurator_pipeline_dwi.png
-	:align: center
+    :align: center
 
-	Panel for configuration of diffusion pipeline stages
+    Panel for configuration of diffusion pipeline stages
 
 Preprocessing
 """"""""""""""
@@ -154,169 +135,159 @@ Preprocessing
 Preprocessing includes denoising, bias field correction, motion and eddy current correction for diffusion data.
 
 .. image:: images/preprocessing.png
-	:align: center
+    :align: center
 
 *Denoising*
 
-	Remove noise from diffusion images using (1) MRtrix3 MP-PCA method or (2) Dipy Non-Local Mean (NLM) denoising with Gaussian or Rician noise models
+    Remove noise from diffusion images using (1) MRtrix3 MP-PCA method or (2) Dipy Non-Local Mean (NLM) denoising with Gaussian or Rician noise models
 
 *Bias field correction*
 
-	Remove intensity inhomogeneities due to the magnetic resonnace bias field using (1) MRtrix3 N4 bias field correction or (2) the bias field correction provided by FSL FAST.
+    Remove intensity inhomogeneities due to the magnetic resonance bias field using (1) MRtrix3 N4 bias field correction or (2) the bias field correction provided by FSL FAST
 
 *Motion correction*
 
-	Aligns diffusion volumes to the b0 volume using FSL's MCFLIRT.
-
-	.. note:: For hemi-sphere DSI aquisitions, warning outputs will be displayed in the console when processing empty volumes.
+    Aligns diffusion volumes to the b0 volume using FSL's MCFLIRT
 
 *Eddy current correction*
 
-	Corrects for eddy current distortions using FSL's Eddy correct tool.
+    Corrects for eddy current distortions using FSL's Eddy correct tool
 
 *Resampling*
 
-	Resample morphological and diffusion data to F0 x F1 x F2 mm^3
+    Resample morphological and diffusion data to F0 x F1 x F2 mm^3
 
 Registration
 """"""""""""""
 
 **Registration mode**
 
-	* FSL (Linear):
-
-		.. image:: images/registration_flirt.png
-			:align: center
-
-	 	Perform linear registration from T1 to diffusion b0 using FSL's flirt.
-
-	* BBregister (FS):
+    * FSL (Linear):
 
-		.. image:: images/registration_fs.png
-			:align: center
+        .. image:: images/registration_flirt.png
+            :align: center
 
-		Perform linear registration using Freesurfer BBregister tool.
+        Perform linear registration from T1 to diffusion b0 using FSL's flirt
 
-	* Non-linear (ANTS):
+    * Non-linear (ANTS):
 
-		.. image:: images/registration_ants.png
-			:align: center
+        .. image:: images/registration_ants.png
+            :align: center
 
-	 	Perform symmetric diffeomorphic SyN registration from T1 to b0
+        Perform symmetric diffeomorphic SyN registration from T1 to diffusion b=0
 
 Diffusion reconstruction and tractography
 """"""""""""""""""""""""""""""""""""""""""""
 
 Perform diffusion reconstruction and local deterministic or probabilistic tractography based on several tools. ROI dilation is required to map brain connections when the tracking only operates in the white matter.
 
-	.. figure:: images/diffusion_config_window.png
-		:align: center
+    .. figure:: images/diffusion_config_window.png
+        :align: center
 
-		Diffusion stage configuration window
+        Diffusion stage configuration window
 
 
 **Reconstruction tool**
 
 
-	**Dipy**: perform SHORE, tensor, CSD and MAP-MRI reconstruction.
+    **Dipy**: perform SHORE, tensor, CSD and MAP-MRI reconstruction
 
-		* SHORE:
+        * SHORE:
 
-			.. image:: images/diffusion_dipy_shore.png
-				:align: center
+            .. image:: images/diffusion_dipy_shore.png
+                :align: center
 
-			SHORE performed only on DSI data
+            SHORE performed only on DSI data
 
-		* Tensor:
+        * Tensor:
 
-			.. image:: images/diffusion_dipy_tensor.png
-				:align: center
+            .. image:: images/diffusion_dipy_tensor.png
+                :align: center
 
-			Tensor performed only on DTI data
+            Tensor performed only on DTI data
 
-		* CSD:
+        * CSD:
 
-			.. image:: images/diffusion_dipy_csd.png
-				:align: center
+            .. image:: images/diffusion_dipy_csd.png
+                :align: center
 
-			CSD performed on DTI and multi-shell data
+            CSD performed on DTI and multi-shell data
 
-		* MAP_MRI:
+        * MAP_MRI:
 
-			.. image:: images/diffusion_dipy_mapmri.png
-				:align: center
+            .. image:: images/diffusion_dipy_mapmri.png
+                :align: center
 
-			MAP-MRI performed only on multi-shell data
+            MAP-MRI performed only on multi-shell data
 
 
-	**MRtrix**: perform CSD reconstruction.
+    **MRtrix**: perform CSD reconstruction.
 
-		* CSD:
+        * CSD:
 
-			.. image:: images/diffusion_mrtrix_csd.png
-				:align: center
+            .. image:: images/diffusion_mrtrix_csd.png
+                :align: center
 
-			CSD performed on DTI and multi-shell data
+            CSD performed on DTI and multi-shell data
 
 
 **Tractography tool**
 
-	**Dipy**: perform deterministic and probabilistic fiber tracking as well as particle filtering tractography.
+    **Dipy**: perform deterministic and probabilistic fiber tracking as well as particle filtering tractography.
 
-		* Deterministic tractography:
+        * Deterministic tractography:
 
-			.. image:: images/diffusion_dipy_deterministic.png
-				:align: center
+            .. image:: images/diffusion_dipy_deterministic.png
+                :align: center
 
-			Deterministic tractography (SD_STREAM) performed on single tensor or CSD reconstruction
+            Deterministic tractography (SD_STREAM) performed on single tensor or CSD reconstruction
 
-		* Probabilistic tractography:
+        * Probabilistic tractography:
 
-			.. image:: images/diffusion_dipy_probabilistic.png
-				:align: center
+            .. image:: images/diffusion_dipy_probabilistic.png
+                :align: center
 
-			Probabilistic tractography (iFOD2) performed on SHORE or CSD reconstruction
+            Probabilistic tractography (iFOD2) performed on SHORE or CSD reconstruction
 
-		* Probabilistic particle filtering tractography (PFT):
+        * Probabilistic particle filtering tractography (PFT):
 
-			.. image:: images/diffusion_dipy_probabilistic_PFT.png
-				:align: center
+            .. image:: images/diffusion_dipy_probabilistic_PFT.png
+                :align: center
 
-			Probabilistic PFT tracking performed on SHORE or CSD reconstruction. Seeding from the gray matter / white matter interface is possible.
+            Probabilistic PFT tracking performed on SHORE or CSD reconstruction. Seeding from the gray matter / white matter interface is possible.
 
-		.. note:: We noticed a shift of the center of tractograms obtained by dipy. As a result, tractograms visualized in TrackVis are not commonly centered despite the fact that the tractogram and the ROIs are properly aligned.
+        .. note:: We noticed a shift of the center of tractograms obtained by dipy. As a result, tractograms visualized in TrackVis are not commonly centered despite the fact that the tractogram and the ROIs are properly aligned.
 
 
-	**MRtrix**: perform deterministic and probabilistic fiber tracking as well as anatomically-constrained tractography. ROI dilation is required to map brain connections when the tracking only operates in the white matter.
+    **MRtrix**: perform deterministic and probabilistic fiber tracking as well as anatomically-constrained tractography. ROI dilation is required to map brain connections when the tracking only operates in the white matter.
 
-		* Deterministic tractography:
+        * Deterministic tractography:
 
-			.. image:: images/diffusion_mrtrix_deterministic.png
-				:align: center
+            .. image:: images/diffusion_mrtrix_deterministic.png
+                :align: center
 
-			Deterministic tractography (SD_STREAM) performed on single tensor or CSD reconstruction
+            Deterministic tractography (SD_STREAM) performed on single tensor or CSD reconstruction
 
-		* Deterministic anatomically-constrained tractography (ACT):
+        * Deterministic anatomically-constrained tractography (ACT):
 
-			.. image:: images/diffusion_mrtrix_deterministic_ACT.png
-				:align: center
+            .. image:: images/diffusion_mrtrix_deterministic_ACT.png
+                :align: center
 
-			Deterministic ACT tracking performed on single tensor or CSD reconstruction. Seeding from the gray matter / white matter interface is possible. Backtrack option is not available in deterministic tracking.
+            Deterministic ACT tracking performed on single tensor or CSD reconstruction. Seeding from the gray matter / white matter interface is possible. Backtrack option is not available in deterministic tracking.
 
-		* Probabilistic tractography:
+        * Probabilistic tractography:
 
-			.. image:: images/diffusion_mrtrix_probabilistic.png
-				:align: center
+            .. image:: images/diffusion_mrtrix_probabilistic.png
+                :align: center
 
-			Probabilistic tractography (iFOD2) performed on SHORE or CSD reconstruction
+            Probabilistic tractography (iFOD2) performed on SHORE or CSD reconstruction
 
-		* Probabilistic anatomically-constrained tractography (ACT):
+        * Probabilistic anatomically-constrained tractography (ACT):
 
-			.. image:: images/diffusion_mrtrix_probabilistic_ACT.png
-				:align: center
-
-			Probabilistic ACT tracking performed on SHORE or CSD reconstruction. Seeding from the gray matter / white matter interface is possible.
+            .. image:: images/diffusion_mrtrix_probabilistic_ACT.png
+                :align: center
 
+            Probabilistic ACT tracking performed on SHORE or CSD reconstruction. Seeding from the gray matter / white matter interface is possible.
 
 Connectome
 """"""""""""""
@@ -324,19 +295,19 @@ Connectome
 Compute fiber length connectivity matrices. If DTI data is processed, FA additional map is computed. In case of DSI, additional maps include GFA and RTOP. In case of MAP-MRI, additional maps are RTPP, RTOP, ...
 
 .. image:: images/connectome.png
-	:align: center
+    :align: center
 
 *Output types*
 
-	Select in which formats the connectivity matrices should be saved.
+    Select in which formats the connectivity matrices should be saved.
 
 FMRI pipeline stages
 ---------------------
 
 .. figure:: images/configurator_pipeline_fmri.png
-	:align: center
+    :align: center
 
-	Panel for configuration of fMRI pipeline stages
+    Panel for configuration of fMRI pipeline stages
 
 Preprocessing
 """"""""""""""
@@ -344,78 +315,78 @@ Preprocessing
 Preprocessing refers to processing steps prior to registration. It includes discarding volumes, despiking, slice timing correction and motion correction for fMRI (BOLD) data.
 
 .. image:: images/preprocessing_fmri.png
-	:align: center
+    :align: center
 
 *Discard n volummes*
 
-	Discard n volumes from further analysis
+    Discard n volumes from further analysis
 
 *Despiking*
 
-	Perform despiking of the BOLD signal using AFNI.
+    Perform despiking of the BOLD signal using AFNI.
 
 *Slice timing and Repetition time*
 
-	Perform slice timing correction using FSL's slicetimer.
+    Perform slice timing correction using FSL's slicetimer.
 
 *Motion correction*
 
-	Align BOLD volumes to the mean BOLD volume using FSL's MCFLIRT.
+    Align BOLD volumes to the mean BOLD volume using FSL's MCFLIRT.
 
 Registration
 """"""""""""""
 
 **Registration mode**
 
-	* FSL (Linear):
+    * FSL (Linear):
 
-		.. image:: images/registration_flirt_fmri.png
-			:align: center
+        .. image:: images/registration_flirt_fmri.png
+            :align: center
 
-		Perform linear registration from T1 to mean BOLD using FSL's flirt.
+        Perform linear registration from T1 to mean BOLD using FSL's flirt.
 
-	* BBregister (FS)
+    * BBregister (FS)
 
-		.. image:: images/registration_fs_fmri.png
-			:align: center
+        .. image:: images/registration_fs_fmri.png
+            :align: center
 
-		Perform linear registration using Freesurfer BBregister tool from T1 to mean BOLD via T2.
+        Perform linear registration using Freesurfer BBregister tool from T1 to mean BOLD via T2.
 
-		.. warning:: development in progress
+        .. warning:: development in progress
 
 fMRI processing
 """""""""""""""""""
 
 Performs detrending, nuisance regression, bandpass filteringdiffusion reconstruction and local deterministic or probabilistic tractography based on several tools. ROI dilation is required to map brain connections when the tracking only operates in the white matter.
 
-
 *Detrending*
 
-	.. image:: images/detrending.png
-		:align: center
+    .. image:: images/detrending.png
+        :align: center
 
-	Detrending of BOLD signal using:
-	1. *linear* trend removal algorithm provided by the `scipy` library
-	2. *quadratic* trend removal algorithm provided by the `obspy` library
+    Detrending of BOLD signal using:
+
+        1. *linear* trend removal algorithm provided by the `scipy` library
+        2. *quadratic* trend removal algorithm provided by the `obspy` library
 
 *Nuisance regression*
 
-	.. image:: images/nuisance.png
-		:align: center
+    .. image:: images/nuisance.png
+        :align: center
 
-	A number of options for removing nuisance signals is provided. They consist of:
-	1. *Global signal* regression
-	2. *CSF* regression
-	3. *WM* regression
-	4. *Motion parameters* regression
+    A number of options for removing nuisance signals is provided. They consist of:
 
-*Bandpass filtering*
+        1. *Global signal* regression
+        2. *CSF* regression
+        3. *WM* regression
+        4. *Motion parameters* regression
 
-	.. image:: images/bandpass.png
-		:align: center
+*Bandpass filtering*
 
-	Perform bandpass filtering of the time-series using FSL's slicetimer
+    .. image:: images/bandpass.png
+        :align: center
 
+    Perform bandpass filtering of the time-series using FSL's slicetimer
 
 Connectome
 """"""""""""""
@@ -423,27 +394,29 @@ Connectome
 Computes ROI-averaged time-series and the correlation connectivity matrices.
 
 .. image:: images/connectome_fmri.png
-	:align: center
+    :align: center
 
 *Output types*
 
-	Select in which formats the connectivity matrices should be saved.
+    Select in which formats the connectivity matrices should be saved.
 
 Save the configuration files
 -------------------------------
 
 You can save the pipeline stage configuration files in two different way:
 
-	1. You can save all configuration files at once by clicking on the `Save All Pipeline Configuration Files`. This  will save automatically the configuration file of the anatomical / diffusion / fMRI pipeline to `<bids_dataset>/code/ref_anatomical_config.ini` / `<bids_dataset>/code/ref_diffusion_config.ini` / `<bids_dataset>/code/ref_fMRI_config.ini` respectively.
+    1. You can save all configuration files at once by clicking on the `Save All Pipeline Configuration Files`. This  will save automatically the configuration file of the anatomical / diffusion / fMRI pipeline to
+       ``<bids_dataset>/code/ref_anatomical_config.ini`` / ``<bids_dataset>/code/ref_diffusion_config.ini`` / ``<bids_dataset>/code/ref_fMRI_config.ini`` respectively.
 
-	2. You can save individually each of the pipeline configuration files and edit its filename in the File menu (File -> Save anatomical/diffusion/fMRI configuration file as...)
+    2. You can save individually each of the pipeline configuration files and edit its filename in the File menu (File -> Save anatomical/diffusion/fMRI configuration file as...)
 
 Nipype
 -------
 
-The Connectome Mapper processing relies on nipype. For each stage, a processing folder is created in $Base_directory/derivatives/nipype/sub-<participant_label>/<pipeline_name>/<stage_name>.
-
-All intermediate steps for the processing are saved in the corresponding stage folders.
+Connectome Mapper relies on Nipype.
+All intermediate steps for the processing are saved in the corresponding
+``<bids_dataset/derivatives>/nipype/sub-<participant_label>/<pipeline_name>/<stage_name>``
+stage folder (See :ref:`Nipype workflow outputs <nipype_outputs>` for more details).
 
 
 Run the BIDS App
@@ -455,90 +428,113 @@ Start the Connectome Mapper BIDS App GUI
 * From the main window, click on the middle button to start the Connectome Mapper BIDS App GUI.
 
 .. image:: images/mainWindow_bidsapp.png
-	:align: center
+    :align: center
 
 * The window of the Connectome Mapper BIDS App GUI will appear, which will help you in setting up and launching the BIDS App run.
 
 .. figure:: images/bidsapp_window.png
-	:align: center
+    :align: center
 
-	Window of the Connectome Mapper BIDS App GUI
+    Window of the Connectome Mapper BIDS App GUI
 
 Run configuration
 -------------------
 
+* Select the output directory for data derivatives
+
+    .. image:: images/bidsapp_select_output.png
+        :align: center
+
 * Select the subject labels to be processed
 
-	.. image:: images/bidsapp_select.png
-		:align: center
+    .. image:: images/bidsapp_select_subject.png
+        :align: center
+
+* Tune the number of subjects to be processed in parallel
+
+    .. image:: images/bidsapp_subject_parallelization.png
+        :align: center
+
+* Tune the advanced execution settings for each subject process. This include finer control on the number of threads used by each process as well as on the seed value of ANTs and MRtrix random number generators.
+
+    .. image:: images/bidsapp_execution_settings.png
+        :align: center
+
+    .. important:: Make sure the number of threads multiplied by the number of subjects being processed in parallel do not exceed the number of CPUs available on your system.
 
 * Check/Uncheck the pipelines to be performed
 
-	.. image:: images/bidsapp_pipeline_check.png
-		:align: center
+    .. image:: images/bidsapp_pipeline_check.png
+        :align: center
 
-* Specify your Freesurfer license
+    .. note:: The list of pipelines might vary as it is automatically updated based on the availability of diffusion MRI and resting-state fMRI data.
 
-	.. image:: images/bidsapp_fslicense.png
-		:align: center
+* Specify your Freesurfer license
 
-	.. note:: Your freesurfer license will be copied to your dataset directory as `<bids_dataset>/code/license.txt` which will be mounted inside the BIDS App container image.
+    .. image:: images/bidsapp_fslicense.png
+        :align: center
 
+    .. note:: Your Freesurfer license will be copied to your dataset directory as `<bids_dataset>/code/license.txt` which will be mounted inside the BIDS App container image.
 
 * When the run is set up, you can click on the `Check settings` button.
 
-	.. image:: images/bidsapp_checksettings.png
-		:align: center
+    .. image:: images/bidsapp_checksettings.png
+        :align: center
 
 * If the setup is complete and valid, this will enable the `Run BIDS App` button.
 
-	.. image:: images/bidsapp_checksettings2.png
-		:align: center
+    .. image:: images/bidsapp_checksettings2.png
+        :align: center
 
 You are ready to launch the BIDS App run!
 
-
 Launch the BIDS App run
 -------------------------
 
 * Click on the `Run BIDS App` button to launch the BIDS App run
 
-	.. image:: images/bidsapp_run.png
-		:align: center
+    .. image:: images/bidsapp_run.png
+        :align: center
 
 * You can see the complete `docker run` command generated by the Connectome Mapper BIDS App GUI from the terminal output such as in this example
-	.. code-block:: console
-
-		Start BIDS App
-		> Copy FreeSurfer license (BIDS App Manager)
-		... src : /usr/local/freesurfer/license.txt
-		... dst : /media/localadmin/HagmannHDD/Seb/ds-testLausanne2008SHOREPFT/code/license.txt
-		> Datalad available: True
-		*... Docker cmd 2 : ['docker', 'run', '-it', '--rm', '-v', '/media/localadmin/HagmannHDD/Seb/ds-testLausanne2008SHOREPFT:/tmp', '-u', '1000:1000', 'sebastientourbier/connectomemapper-bidsapp:3.0.0-beta-singularity', '/tmp', '/tmp/derivatives', 'participant', '--participant_label', 'A001', '--anat_pipeline_config', '/tmp/code/ref_anatomical_config.ini', '--dwi_pipeline_config', '/tmp/code/ref_diffusion_config.ini']*
-		> BIDS dataset: /tmp
-		> Subjects to analyze : ['A001']
-		> Copy FreeSurfer license (BIDS App)
-		> Sessions to analyze : ['ses-20150203160809']
-		> Process subject sub-A001 session ses-20150203160809
-		WARNING: rewriting config file /tmp/derivatives/sub-A001_ses-20150203160809_anatomical_config.ini
-		... Anatomical config created : /tmp/derivatives/sub-A001_ses-20150203160809_anatomical_config.ini
-		WARNING: rewriting config file /tmp/derivatives/sub-A001_ses-20150203160809_diffusion_config.ini
-		... Diffusion config created : /tmp/derivatives/sub-A001_ses-20150203160809_diffusion_config.ini
-		... Running pipelines :
-		        - Anatomical MRI (segmentation and parcellation)
-		        - Diffusion MRI (structural connectivity matrices)
-		... cmd : connectomemapper3 /tmp /tmp/derivatives sub-A001 ses-20150203160809 /tmp/derivatives/sub-A001_ses-20150203160809_anatomical_config.ini True /tmp/derivatives/sub-A001_ses-20150203160809_diffusion_config.ini True
-
-	.. note:: Also, this can be helpful in you wish to design your own batch scripts to call the BIDS App with the correct syntax.
-
 
+    .. code-block:: console
+
+        Start BIDS App
+        > FreeSurfer license copy skipped as it already exists (BIDS App Manager)
+        > Datalad available: True
+        ... BIDS App execution command: ['docker', 'run', '-it', '--rm', '-v', '/home/localadmin/Desktop/hcp-retest-d2:/bids_dir', '-v', '/home/localadmin/Desktop/hcp-retest-d2/derivatives:/output_dir', '-v', '/usr/local/freesurfer/license.txt:/bids_dir/code/license.txt', '-v', '/home/localadmin/Desktop/hcp-retest-d2/code/ref_anatomical_config.ini:/code/ref_anatomical_config.ini', '-v', '/home/localadmin/Desktop/hcp-retest-d2/code/ref_diffusion_config.ini:/code/ref_diffusion_config.ini', '-v', '/home/localadmin/Desktop/hcp-retest-d2/code/ref_fMRI_config.ini:/code/ref_fMRI_config.ini', '-u', '1000:1000', 'sebastientourbier/connectomemapper-bidsapp:v3.0.0-RC3', '/bids_dir', '/output_dir', 'participant', '--participant_label', '103818', '--anat_pipeline_config', '/code/ref_anatomical_config.ini', '--dwi_pipeline_config', '/code/ref_diffusion_config.ini', '--func_pipeline_config', '/code/ref_fMRI_config.ini', '--fs_license', '/bids_dir/code/license.txt', '--number_of_participants_processed_in_parallel', '1', '--number_of_threads', '10', '--ants_number_of_threads', '10']
+        > BIDS dataset: /bids_dir
+        > Subjects to analyze : ['103818']
+        > Set $FS_LICENSE which points to FreeSurfer license location (BIDS App)
+          ... $FS_LICENSE : /bids_dir/code/license.txt
+          * Number of subjects to be processed in parallel set to 1 (Total of cores available: 11)
+          * Number of parallel threads set to 10 (total of cores: 11)
+          * OMP_NUM_THREADS set to 10 (total of cores: 11)
+          * ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS set to 10
+        Report execution to Google Analytics.
+        Thanks to support us in the task of finding new funds for CMP3 development!
+        > Sessions to analyze : ['ses-01']
+        > Process subject sub-103818 session ses-01
+        WARNING: rewriting config file /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_anatomical_config.ini
+        ... Anatomical config created : /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_anatomical_config.ini
+        WARNING: rewriting config file /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_diffusion_config.ini
+        ... Diffusion config created : /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_diffusion_config.ini
+        WARNING: rewriting config file /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_fMRI_config.ini
+        ... fMRI config created : /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_fMRI_config.ini
+        ... Running pipelines :
+                - Anatomical MRI (segmentation and parcellation)
+                - Diffusion MRI (structural connectivity matrices)
+                - fMRI (functional connectivity matrices)
+        ... cmd : connectomemapper3 --bids_dir /bids_dir --output_dir /output_dir --participant_label sub-103818 --session_label ses-01 --anat_pipeline_config /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_anatomical_config.ini --dwi_pipeline_config /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_diffusion_config.ini --func_pipeline_config /output_dir/cmp/sub-103818/ses-01/sub-103818_ses-01_fMRI_config.ini --number_of_threads 10
+
+    .. note:: Also, this can be helpful in you wish to design your own batch scripts to call the BIDS App with the correct syntax.
 
 Check progress
 ------------------
 
 For each subject, the execution output of the pipelines are redirected to a log file, written as ``<bids_dataset/derivatives>/cmp/sub-<subject_label>_log.txt``. Execution progress can be checked by the means of these log files.
 
-
 Check stages outputs
 ******************************
 
@@ -548,115 +544,113 @@ Start the Inspector Window
 * From the main window, click on the right button to start the Inspector Window.
 
 .. image:: images/mainWindow_outputs.png
-	:align: center
+    :align: center
 
 * The window of the Connectome Mapper BIDS App Inspector will appear, which will assist you in inspecting outputs of the different pipeline stages (each pipeline has a tab panel).
 
-
 Anatomical pipeline stages
 ---------------------------
 
 * Click on the stage you wish to check the output(s):
 
-	.. figure:: images/outputcheck_pipeline_anat.png
-		:align: center
+    .. figure:: images/outputcheck_pipeline_anat.png
+        :align: center
 
-		Panel for configuration of anatomical pipeline stages
+        Panel for configuration of anatomical pipeline stages
 
 Segmentation
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_seg.png
-		:align: center
+    .. image:: images/outputcheck_stage_seg.png
+        :align: center
 
 **Segmentation results**
 
 Surfaces extracted using Freesurfer.
 
 .. image:: images/ex_segmentation1.png
-	:width: 600
+    :width: 600
 
 T1 segmented using Freesurfer.
 
 .. image:: images/ex_segmentation2.png
-	:width: 600
+    :width: 600
 
 Parcellation
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_parc.png
-		:align: center
+    .. image:: images/outputcheck_stage_parc.png
+        :align: center
 
 **Parcellation results**
 
 Cortical and subcortical parcellation are shown with Freeview.
 
 .. image:: images/ex_parcellation2.png
-	:width: 600
+    :width: 600
 
 Diffusion pipeline stages
 ---------------------------
 
 * Click on the stage you wish to check the output(s):
 
-	.. figure:: images/outputcheck_pipeline_dwi.png
-		:align: center
+    .. figure:: images/outputcheck_pipeline_dwi.png
+        :align: center
 
-		Panel for configuration of diffusion pipeline stages
+        Panel for configuration of diffusion pipeline stages
 
 Preprocessing
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_prep.png
-		:align: center
-
+    .. image:: images/outputcheck_stage_prep.png
+        :align: center
 
 Registration
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_reg.png
-		:align: center
+    .. image:: images/outputcheck_stage_reg.png
+        :align: center
 
 **Registration results**
 
 Registration of T1 to Diffusion space (b0). T1 in copper overlayed to the b0 image.
 
 .. image:: images/ex_registration.png
-	:width: 600
+    :width: 600
 
 Diffusion reconstruction and tractography
 """"""""""""""""""""""""""""""""""""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_dwi.png
-		:align: center
+    .. image:: images/outputcheck_stage_dwi.png
+        :align: center
 
 **Tractography results**
 
 DSI Tractography results are displayed with TrackVis.
 
 .. image:: images/ex_tractography1.png
-	:width: 600
+    :width: 600
 
 .. image:: images/ex_tractography2.png
-	:width: 600
+    :width: 600
 
 Connectome
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_conn.png
-		:align: center
+    .. image:: images/outputcheck_stage_conn.png
+        :align: center
 
 **Generated connection matrix**
 
@@ -665,62 +659,59 @@ Displayed using a:
 1. matrix layout with pyplot
 
 .. image:: images/ex_connectionmatrix.png
-	:width: 600
+    :width: 600
 
 2. circular layout with pyplot and MNE
 
 .. image:: images/ex_connectioncircular.png
-	:width: 600
-
+    :width: 600
 
 FMRI pipeline stages
 ---------------------
 
 * Click on the stage you wish to check the output(s):
 
-	.. figure:: images/outputcheck_pipeline_fmri.png
-		:align: center
+    .. figure:: images/outputcheck_pipeline_fmri.png
+        :align: center
 
-		Panel for configuration of fMRI pipeline stages
+        Panel for configuration of fMRI pipeline stages
 
 Preprocessing
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_prep_fmri.png
-		:align: center
-
+    .. image:: images/outputcheck_stage_prep_fmri.png
+        :align: center
 
 Registration
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_reg_fmri.png
-		:align: center
-
+    .. image:: images/outputcheck_stage_reg_fmri.png
+        :align: center
 
 fMRI processing
 """""""""""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_func.png
-		:align: center
+    .. image:: images/outputcheck_stage_func.png
+        :align: center
 
 **ROI averaged time-series**
 
-	.. image:: images/ex_rsfMRI.png
-		:width: 600
+    .. image:: images/ex_rsfMRI.png
+        :width: 600
 
 Connectome
 """"""""""""""
 
 * Select the desired output from the list and click on `view`:
 
-	.. image:: images/outputcheck_stage_conn_fmri.png
-		:align: center
+    .. image:: images/outputcheck_stage_conn_fmri.png
+        :align: center
 
 **Generated connection matrix**
 
@@ -729,9 +720,9 @@ Displayed using a:
 1. matrix layout with pyplot
 
 .. image:: images/ex_connectionmatrix_fmri.png
-	:width: 600
+    :width: 600
 
 2. circular layout with pyplot and MNE
 
 .. image:: images/ex_connectioncircular_fmri.png
-	:width: 600
\ No newline at end of file
+    :width: 600
diff --git a/docs/changes.rst b/docs/changes.rst
index da5b85cca..a33833b5d 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -2,6 +2,45 @@
 Changes
 ========
 
+****************************
+Version 3.0.0-RC3
+****************************
+
+Date: February 05, 2021
+
+This version corresponds to the third release candidate of Connectome Mapper 3.
+In particular, it integrates `Pull Request #62 <https://github.com/connectomicslab/connectomemapper3/pull/62>`_ which includes:
+
+*Updates*
+
+* MRtrix3 has been updated from `3.0_RC3_latest` to `3.0.2`.
+* Numpy has been updated from `1.18.5` to `1.19.2`.
+* Nipype has been updated to `1.5.0` to `1.5.1`.
+* Dipy has been updated from `1.0.0` to `1.3.0`.
+* CVXPY has been updated from `1.1.5` to `1.1.7`.
+
+*Documentation*
+
+* Update outdated screenshots for GUI documentation page at `readthedocs <https://connectome-mapper-3.readthedocs.io/en/latest/api_doc.html>`_ reported at `CMTK user-group <https://groups.google.com/g/cmtk-users/c/oSjqfjiTcmg/m/4PHLDpPSCwAJ>`_.
+* Correction of multiple typos.
+
+*Bug fixes*
+
+* Update code for Dipy tracking with DTI model following major changes in Dipy 1.0 (Fix reported issue `#54 <https://github.com/connectomicslab/connectomemapper3/issues/54>`_).
+* Update to Dipy 1.3.0 has removed the deprecated warnings related to CVXPY when using MAP_MRI (`#63 <https://github.com/connectomicslab/connectomemapper3/issues/63>`_)
+* Do not set anymore `OMP_NUM_THREADS` at execution due to allocation errors raised when using numpy function dot in Dipy.
+
+*Software development life cycle*
+
+* Add `Test 08` that runs anatomical and fMRI pipelines with:
+  Lausanne2018 parcellation, FSL FLIRT co-registration, all nuisance regression, linear detrending and scrubbing
+* Add `Test 09` that runs anatomical and dMRI pipelines with:
+  Lausanne2018 parcellation, FSL FLIRT, Dipy SHORE, MRtrix SD_Stream tracking, MRtrix SIFT tractogram filtering
+* Remove `deploy_singularity_latest` from the workflow for the sake of space on Sylabs.io.
+
+Please check the `main pull request 62 page <https://github.com/connectomicslab/connectomemapper3/pull/62>`_ for more details.
+
+
 ****************************
 Version 3.0.0-RC2-patch1
 ****************************
diff --git a/docs/images/bidsapp_checksettings.png b/docs/images/bidsapp_checksettings.png
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index e2147c851..78e9f3ef9 100644
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diff --git a/docs/images/diffusion_mrtrix_probabilistic_ACT.png b/docs/images/diffusion_mrtrix_probabilistic_ACT.png
index 9f7c986ac..9ae459df6 100644
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diff --git a/docs/images/segmentation_fs.png b/docs/images/segmentation_fs.png
index 2bb2de406..0e7aa72ac 100644
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diff --git a/docs/installation.rst b/docs/installation.rst
index 5f5311a58..7e66f1ff5 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -123,20 +123,23 @@ The installation of the Connectome Mapper 3 BIDS App Manager (CMPBIDSAPPManager)
 
   .. parsed-literal::
 
+    $ cd connectomemapper3
     $ git fetch
     $ git checkout tags/|release| -b |release|
 
+.. note::
+  If a few bugs related to the Graphical User Interface were fixed after releasing the version, you might want to use the code at its latest version on the master branch (i.e. ``git checkout master``).
+
 * Create a miniconda3 environment where all python dependencies will be installed, this by using the spec list "conda_packages_list.txt" provided by the repository::
 
-	$ conda env create -f connectomemapper3/environment.yml
+    $ cd connectomemapper3
+    $ conda env create -f environment.yml
 
 .. important::
-  It seems there is no conda package for `git-annex` available on Mac.
-  Git-annex should be installed on MacOSX using brew (https://brew.sh/index_fr) i.e. ``brew install git-annex``.
-
-  Note that `git-annex` is only necessary if you wish to use BIDS datasets managed by Datalad (https://www.datalad.org/), a very experimental feature. For the moment, I would not recommend to use right now as it has been a long time it has not been tested.
+  It seems there is no conda package for `git-annex` available on Mac. For your convenience, we created an additional `environment_macosx.yml` miniconda3 environment where the line `- git-annex=7.20190219` has been removed.
+  Git-annex should be installed on MacOSX using brew (https://brew.sh/index_fr) i.e. ``brew install git-annex``. See https://git-annex.branchable.com/install/ for more details.
 
-  So, you can without any problem delete or comment the line `- git-annex=7.20190219` and all other lines related to datalad packages in the `environment.yml` and it should then work!
+  Note that `git-annex` is only necessary if you wish to use BIDS datasets managed by Datalad (https://www.datalad.org/), a very experimental feature still in beta-testing phase.
 
 * Activate the conda environment::
 
diff --git a/docs/outputs.rst b/docs/outputs.rst
index 72cb4e72e..60c4906c4 100644
--- a/docs/outputs.rst
+++ b/docs/outputs.rst
@@ -4,6 +4,30 @@ Outputs of Connectome Mapper 3
 
 Processed, or derivative, data are outputed to ``<bids_dataset/derivatives>/``.
 
+BIDS derivatives entities
+--------------------------
+
+.. tabularcolumns:: |l|p{5cm}|
+
++--------------------------+------------------------------------------------------------------------------------------------------------+
+| **Entity**               | **Description**                                                                                            |
++==========================+============================================================================================================+
+| ``sub-<label>``          | Distinguish different subjects                                                                             |
++--------------------------+------------------------------------------------------------------------------------------------------------+
+| ``ses-<label>``          | Distinguish different acquisition sessions                                                                 |
++--------------------------+------------------------------------------------------------------------------------------------------------+
+| ``label-<label>``        | Describe the type of brain tissue segmented (for _probseg/dseg) or the parcellation atlas (for _atlas)     |
++--------------------------+------------------------------------------------------------------------------------------------------------+
+| ``space-DWI``            | Distinguish anatomical MRI derivatives in the target diffusion MRI space                                   |
++--------------------------+------------------------------------------------------------------------------------------------------------+
+| ``model-<label>``        | Distinguish different diffusion signal models (DTI, CSD, SHORE, MAPMRI)                                    |
++--------------------------+------------------------------------------------------------------------------------------------------------+
+
+See `Original BIDS Entities Appendix <https://bids-specification.readthedocs.io/en/v1.4.1/99-appendices/09-entities.html>`_ for more description.
+
+.. note:: A new suffix `_atlas` has been introduced, that is used in combination with the ``label-<atlas_label>`` entity (where ``<atlas_label>``:``Desikan``/``L2008``/``L2018``) to distinguish different parcellation atlas outputs.
+
+
 Main Connectome Mapper Derivatives
 ==========================================
 
@@ -133,7 +157,7 @@ Diffusion derivatives in the individual ``DWI`` space are placed in each subject
     where:
 
     - ``<model_label>`` is the diffusion model used to drive tractography (DTI, CSD, SHORE)
-    - ``<model_label>`` is the type of tractography algorithm employed (DET for deterministic, PROB for probabilistic)
+    - ``<label>`` is the type of tractography algorithm employed (DET for deterministic, PROB for probabilistic)
 
 * The structural connectivity (SC) graphs:
 
@@ -216,6 +240,9 @@ A FreeSurfer subjects directory is created in ``<bids_dataset/derivatives>/frees
 
 The ``fsaverage`` subject distributed with the running version of FreeSurfer is copied into this directory.
 
+
+.. _nipype_outputs:
+
 Nipype Workflow Derivatives
 ==========================================
 
diff --git a/environment_macosx.yml b/environment_macosx.yml
new file mode 100644
index 000000000..5cb6d703f
--- /dev/null
+++ b/environment_macosx.yml
@@ -0,0 +1,43 @@
+name: py37cmp-gui
+
+channels:
+- aramislab
+- anaconda
+- conda-forge
+- conda-forge/label/cf201901
+- defaults
+
+dependencies:
+- python=3.7
+- pip=20.1.1
+- numpy=1.18.5 # =1.15.4
+- matplotlib=3.2.2 # =2.2.3
+- traits=6.0.0 # =5.1
+- traitsui=6.1.3 # =6.0.0
+- graphviz=2.40.1 # =2.40.1
+- nipype=1.5.0 # =1.5.0
+- 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.* # requirements of fsleyes
+
+- pip:
+    #- cfflib==2.0.5
+    # - git+https://github.com/LTS5/cfflib.git
+    - duecredit==0.8.0 # ==0.7.0
+    - dipy==1.1.1 # ==0.15.0
+    - mne==0.20.7 # ==0.17.1
+    - obspy==1.2.1 # ==1.1.1
+    - datalad[full]==0.13.0 # ==0.11.4
+    # - datalad-revolution==0.6.0
+    - datalad-container==0.3.1
+    - datalad_neuroimaging==0.2.0
+    - pybids==0.10.2 # ==0.9.5
+    - apptools==4.5.0
+    - statsmodels==0.11.1 # ==0.9.0
+    - networkx==2.2
+    - sphinx==3.1.1 # ==1.8.5
+    - sphinx_rtd_theme==0.5.0 # ==0.4.3
+    - sphinx-argparse==0.2.5 # ==0.2.5
+    - recommonmark==0.6.0 # ==0.5.0
+    - pydicom==2.0.0 # ==1.4.2
diff --git a/run.py b/run.py
index b0968b7ca..297a44df5 100644
--- a/run.py
+++ b/run.py
@@ -17,7 +17,6 @@
 import warnings
 
 from glob import glob
-import numpy
 
 # import http.client
 # import urllib
@@ -103,22 +102,18 @@ def create_cmp_command(project, run_anat, run_dmri, run_fmri, number_of_threads=
         If True, append the fMRI configuration file to the command
 
     number_of_threads : int
-        Number of threads used by Nipype
+        Number of threads used OpenMP-parallelized tools
+        (Default: 1)
 
     Returns
     -------
     Command : string
         The command to execute the `connectomemapper3` python script
     """
-    cmd = []
-
-    cmd.append("connectomemapper3")
-    cmd.append("--bids_dir")
-    cmd.append(project.base_directory)
-    cmd.append("--output_dir")
-    cmd.append(project.output_directory)
-    cmd.append("--participant_label")
-    cmd.append(project.subject)
+    cmd = ["connectomemapper3",
+           "--bids_dir", project.base_directory,
+           "--output_dir", project.output_directory,
+           "--participant_label", project.subject]
 
     if project.subject_session != '':
         cmd.append("--session_label")
@@ -343,9 +338,7 @@ def run(command, env={}, log_filename={}):
     #     raise Exception("Non zero return code: %d"%process.returncode)
 
 
-# Initialize random generator for enhanced reproducibility
-numpy.random.seed(1234)
-
+# Parse script arguments
 cmp_parser = parser.get()
 args = cmp_parser.parse_args()
 
@@ -381,7 +374,7 @@ def run(command, env={}, log_filename={}):
 # Make sure freesurfer is happy with the license
 print('> Set $FS_LICENSE which points to FreeSurfer license location (BIDS App)')
 
-if os.access(os.path.join('/bids_dir¨', 'code', 'license.txt'), os.F_OK):
+if os.access(os.path.join('/bids_dir', 'code', 'license.txt'), os.F_OK):
     os.environ['FS_LICENSE'] = os.path.join('/bids_dir', 'code', 'license.txt')
     # Not anymore needed as we are using the environment variable
     # print('... src : {}'.format(os.path.join('/tmp','code','license.txt')))
@@ -434,7 +427,7 @@ def run(command, env={}, log_filename={}):
     print('  * Number of subjects to be processed in parallel set to one (sequential run)')
     parallel_number_of_subjects = 1
 
-# Setup number of threads to be used fro multithreading by OpenMP
+# Setup number of threads to be used for multithreading by OpenMP
 if args.number_of_threads is not None:
     number_of_threads = int(args.number_of_threads)
     if parallel_number_of_subjects == 1:
@@ -475,17 +468,21 @@ def run(command, env={}, log_filename={}):
 
 # Set number of threads used by programs based on OpenMP multi-threading library
 # This includes AFNI, Dipy, Freesurfer, FSL, MRtrix3.
-os.environ['OMP_NUM_THREADS'] = '{}'.format(number_of_threads)
-print('  * OMP_NUM_THREADS set to {} (total of cores: {})'.format(os.environ['OMP_NUM_THREADS'], max_number_of_cores))
+# os.environ.update(OMP_NUM_THREADS=f'{number_of_threads}')
+# print('  * OMP_NUM_THREADS set to {} (total of cores: {})'.format(os.environ['OMP_NUM_THREADS'], max_number_of_cores))
 
 # Set number of threads used by ANTs if specified.
 # Otherwise use the same as the number of OpenMP threads
 if args.ants_number_of_threads is not None:
     os.environ['ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS'] = f'{args.ants_number_of_threads}'
     print(f'  * ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS set to {os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"]}')
-else:
-    os.environ['ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS'] = os.environ['OMP_NUM_THREADS']
-    print(f'  * ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS set to {os.environ["ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS"]}')
+
+# Initialize random generator for enhanced reproducibility
+# Numpy needs to be imported after setting the different multi-threading environment variable
+# See https://stackoverflow.com/questions/30791550/limit-number-of-threads-in-numpy for more details
+# noinspection PyPep8
+import numpy
+numpy.random.seed(1234)
 
 # Set random generator seed of MRtrix if specified
 if args.mrtrix_random_seed is not None:
diff --git a/scripts/bidsapp/run_cmp3.sh b/scripts/bidsapp/run_cmp3.sh
index 86531971a..c2b48b3a5 100644
--- a/scripts/bidsapp/run_cmp3.sh
+++ b/scripts/bidsapp/run_cmp3.sh
@@ -1,8 +1,4 @@
 #!/bin/bash
-echo User: $(id -un $USER) && echo Group: $(id -gn $USER) &&
 . "$FSLDIR/etc/fslconf/fsl.sh" &&
-export && \
-echo "SHELL: $SHELL" && \
-echo "PATH: $PATH" && \
 . activate "${CONDA_ENV}" &&
 xvfb-run -s "-screen 0 900x900x24 -ac +extension GLX -noreset" -a python /app/connectomemapper3/run.py "$@"
diff --git a/scripts/bidsappmanager/cmpbidsappmanager b/scripts/bidsappmanager/cmpbidsappmanager
index 12ef0ad4f..1e095b898 100644
--- a/scripts/bidsappmanager/cmpbidsappmanager
+++ b/scripts/bidsappmanager/cmpbidsappmanager
@@ -29,7 +29,7 @@ def usage():
 
 
 # Checks the needed dependencies. We call directly the functions instead
-# of just checking existence in $PATH in order to handl missing libraries.
+# of just checking existence in $PATH in order to handle missing libraries.
 # Note that not all the commands give the awaited 1 exit code...
 def dep_check():
     """Check if some dependencies are well installed."""
@@ -55,7 +55,7 @@ if __name__ == "__main__":
     info()
 
     argc = len(sys.argv)
-    if argc==1: # no args, launch the GUI
+    if argc == 1:  # no args, launch the GUI
         mw = gui.CMP_MainWindow()
         mw_res = mw.configure_traits()
     else:
diff --git a/scripts/connectomemapper3 b/scripts/connectomemapper3
index 6a88e7cf8..d946b1d24 100644
--- a/scripts/connectomemapper3
+++ b/scripts/connectomemapper3
@@ -107,19 +107,18 @@ def create_parser():
     return p
 
 
-
 if __name__ == "__main__":
-
+    # Parse script arguments
     parser = create_parser()
     args = parser.parse_args()
 
-    # check dependencies
+    # Check dependencies
     dep_check()
 
-    # add current directory to the path, useful if DTB_ bins not installed
+    # Add current directory to the path, useful if DTB_ bins not installed
     os.environ["PATH"] += os.pathsep + os.path.dirname(sys.argv[0])
 
-    # version and copyright message
+    # Version and copyright message
     info()
 
     project = cmp.project.CMP_Project_Info()
@@ -153,7 +152,7 @@ if __name__ == "__main__":
             anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
             
             if args.number_of_threads is not None:
-                print('--- Set Freesurfer and ANTs to use {} threads by the means of OpenMP'.format(args.number_of_threads))
+                print(f'--- Set Freesurfer and ANTs to use {args.number_of_threads} threads by the means of OpenMP')
                 anat_pipeline.stages['Segmentation'].config.number_of_threads = args.number_of_threads
 
             if anat_valid_inputs:
@@ -172,7 +171,7 @@ if __name__ == "__main__":
             anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
 
             if args.number_of_threads is not None:
-                print('--- Set Freesurfer and ANTs to use {} threads by the means of OpenMP'.format(args.number_of_threads))
+                print(f'--- Set Freesurfer and ANTs to use {args.number_of_threads} threads by the means of OpenMP')
                 anat_pipeline.stages['Segmentation'].config.number_of_threads = args.number_of_threads
 
             if anat_valid_inputs:
@@ -191,7 +190,7 @@ if __name__ == "__main__":
             if dmri_pipeline is not None:
                 dmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
                 dmri_pipeline.atlas_info = anat_pipeline.atlas_info
-                #print sys.argv[offset+7]
+                # print sys.argv[offset+7]
                 if dmri_valid_inputs:
                     dmri_pipeline.process()
                 else:
@@ -211,7 +210,7 @@ if __name__ == "__main__":
             anat_valid_inputs = anat_pipeline.check_input(bids_layout,gui=False)
             
             if args.number_of_threads is not None:
-                print('--- Set Freesurfer and ANTs to use {} threads by the means of OpenMP'.format(args.number_of_threads))
+                print(f'--- Set Freesurfer and ANTs to use {args.number_of_threads} threads by the means of OpenMP')
                 anat_pipeline.stages['Segmentation'].config.number_of_threads = args.number_of_threads
 
             if anat_valid_inputs:
@@ -230,10 +229,10 @@ if __name__ == "__main__":
             if fmri_pipeline is not None:
                 fmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
                 fmri_pipeline.atlas_info = anat_pipeline.atlas_info
-                #fmri_pipeline.subjects_dir = anat_pipeline.stages['Segmentation'].config.freesurfer_subjects_dir
-                #fmri_pipeline.subject_id = anat_pipeline.stages['Segmentation'].config.freesurfer_subject_id
-                #print('Freesurfer subjects dir: {}'.format(fmri_pipeline.subjects_dir))
-                #print('Freesurfer subject id: {}'.format(fmri_pipeline.subject_id))
+                # fmri_pipeline.subjects_dir = anat_pipeline.stages['Segmentation'].config.freesurfer_subjects_dir
+                # fmri_pipeline.subject_id = anat_pipeline.stages['Segmentation'].config.freesurfer_subject_id
+                # print('Freesurfer subjects dir: {}'.format(fmri_pipeline.subjects_dir))
+                # print('Freesurfer subject id: {}'.format(fmri_pipeline.subject_id))
 
                 # print sys.argv[offset+9]
                 if fmri_valid_inputs:
@@ -257,7 +256,7 @@ if __name__ == "__main__":
             anat_valid_inputs = anat_pipeline.check_input(bids_layout,gui=False)
             
             if args.number_of_threads is not None:
-                print('--- Set Freesurfer and ANTs to use {} threads by the means of OpenMP'.format(args.number_of_threads))
+                print(f'--- Set Freesurfer and ANTs to use {args.number_of_threads} threads by the means of OpenMP')
                 anat_pipeline.stages['Segmentation'].config.number_of_threads = args.number_of_threads
 
             if anat_valid_inputs:
@@ -290,8 +289,8 @@ if __name__ == "__main__":
                 fmri_pipeline.atlas_info = anat_pipeline.atlas_info
                 fmri_pipeline.subjects_dir = anat_pipeline.stages['Segmentation'].config.freesurfer_subjects_dir
                 fmri_pipeline.subject_id = anat_pipeline.stages['Segmentation'].config.freesurfer_subject_id
-                print('Freesurfer subjects dir: {}'.format(fmri_pipeline.subjects_dir))
-                print('Freesurfer subject id: {}'.format(fmri_pipeline.subject_id))
+                print(f'Freesurfer subjects dir: {fmri_pipeline.subjects_dir}')
+                print(f'Freesurfer subject id: {fmri_pipeline.subject_id}')
 
                 # print sys.argv[offset+9]
                 if fmri_valid_inputs:
@@ -303,174 +302,3 @@ if __name__ == "__main__":
         else:
             print(msg)
             sys.exit(1)
-
-
-
-# Old version with sys.argv for managing script arguments
-#     argc = len(sys.argv)
-
-#     if (argc==6) or (argc==7): # connectomemapper bids_folder output_dir sub-<label> (ses-<label>) anatomical_ini_file process_anatomical
-
-#         project = cmp.project.CMP_Project_Info()
-#         project.base_directory = os.path.abspath(sys.argv[1])
-#         project.output_directory = os.path.abspath(sys.argv[2])
-#         project.subjects = ['%s' % sys.argv[3]]
-#         project.subject = '%s' % sys.argv[3]
-
-#         try:
-#             bids_layout = BIDSLayout(project.base_directory)
-#         except:
-#             print("Exception : Raised at BIDSLayout")
-#             sys.exit(1)
-
-#         if "ses-" in sys.argv[4]:
-#             offset = 1
-#             project.subject_sessions = ['%s' % sys.argv[4]]
-#             project.subject_session = '%s' % sys.argv[4]
-#             print("INFO : Detected session(s)")
-#         else:
-#             print("INFO : No detected session")
-#             offset = 0
-#             project.subject_sessions = ['']
-#             project.subject_session = ''
-
-#         project.anat_config_file = os.path.abspath(sys.argv[offset+4])
-
-#         anat_pipeline = cmp.project.init_anat_project(project, False)
-#         if anat_pipeline is not None:
-#             anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
-#             if anat_valid_inputs and sys.argv[offset+5]:
-#                 anat_pipeline.process()
-#             elif anat_valid_inputs and sys.argv[offset+5]=='False':
-#                 pass
-#             else:
-#                 sys.exit(1)
-
-#     elif (argc==8) or (argc==9): # connectomemapper bids_folder output_dir sub-<label> (ses-<label>) anatomical_ini_file process_anatomical diffusion_ini_file process_diffusion
-
-#         project = cmp.project.CMP_Project_Info()
-#         project.base_directory = os.path.abspath(sys.argv[1])
-#         project.output_directory = os.path.abspath(sys.argv[2])
-#         project.subjects = ['%s' % sys.argv[3]]
-#         project.subject = '%s' % sys.argv[3]
-
-#         try:
-#             bids_layout = BIDSLayout(project.base_directory)
-#         except:
-#             sys.exit(1)
-
-#         if "ses-" in sys.argv[4]:
-#             offset = 1
-#             project.subject_sessions = ['%s' % sys.argv[4]]
-#             project.subject_session = '%s' % sys.argv[4]
-#         else:
-#             offset = 0
-#             project.subject_sessions = ['']
-#             project.subject_session = ''
-
-#         project.anat_config_file = os.path.abspath(sys.argv[offset+4])
-#         project.dmri_config_file = os.path.abspath(sys.argv[offset+6])
-
-#         anat_pipeline = cmp.project.init_anat_project(project, False)
-#         if anat_pipeline is not None:
-#             anat_valid_inputs = anat_pipeline.check_input(bids_layout, gui=False)
-
-#             if anat_valid_inputs and sys.argv[offset+5]=='True':
-#                 print(">> Process anatomical pipeline")
-#                 anat_pipeline.process()
-#             elif anat_valid_inputs and sys.argv[offset+5]=='False':
-#                 print(">> Collecting precomputed anatomical pipeline")
-#                 pass
-#             else:
-#                 print("ERROR : Invalid inputs")
-#                 sys.exit(1)
-
-#         anat_valid_outputs, msg = anat_pipeline.check_output()
-
-#         if anat_valid_outputs:
-#             dmri_valid_inputs, dmri_pipeline = cmp.project.init_dmri_project(project, bids_layout, False)
-#             if dmri_pipeline is not None:
-#                 dmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
-#                 dmri_pipeline.atlas_info = anat_pipeline.atlas_info
-#                 #print sys.argv[offset+7]
-#                 if dmri_valid_inputs and sys.argv[offset+7]=='True':
-#                     dmri_pipeline.process()
-#                 else:
-#                     sys.exit(1)
-#         else:
-#             print msg
-#             sys.exit(1)
-
-#     elif (argc==10) or (argc==11): # connectomemapper bids_folder output_dir sub-<label> (ses-<label>) anatomical_ini_file process_anatomical diffusion_ini_file process_diffusion fmri_ini_file process_fmri
-
-#         project = cmp.project.CMP_Project_Info()
-#         project.base_directory = os.path.abspath(sys.argv[1])
-#         project.output_directory = os.path.abspath(sys.argv[2])
-#         project.subjects = ['%s' % sys.argv[3]]
-#         project.subject = '%s' % sys.argv[3]
-
-#         try:
-#             bids_layout = BIDSLayout(project.base_directory)
-#         except:
-#             print("Exception : {}".format(project.base_directory))
-#             print("Exception : {}".format(bids_layout))
-#             sys.exit(1)
-
-#         if "ses-" in sys.argv[4]:
-#             offset = 1
-#             project.subject_sessions = ['%s' % sys.argv[4]]
-#             project.subject_session = '%s' % sys.argv[4]
-#         else:
-#             offset = 0
-#             project.subject_sessions = ['']
-#             project.subject_session = ''
-
-#         project.anat_config_file = os.path.abspath(sys.argv[offset+4])
-#         project.dmri_config_file = os.path.abspath(sys.argv[offset+6])
-#         project.fmri_config_file = os.path.abspath(sys.argv[offset+8])
-
-#         anat_pipeline = cmp.project.init_anat_project(project, False)
-#         if anat_pipeline is not None:
-#             anat_valid_inputs = anat_pipeline.check_input(bids_layout,gui=False)
-
-#             if anat_valid_inputs and sys.argv[offset+5]=='True':
-#                 print(">> Process anatomical pipeline")
-#                 anat_pipeline.process()
-#             elif anat_valid_inputs and sys.argv[offset+5]=='False':
-#                 print(">> Collecting precomputed anatomical pipeline")
-#                 pass
-#             else:
-#                 print("ERROR : Invalid inputs")
-#                 sys.exit(1)
-
-#         anat_valid_outputs, msg = anat_pipeline.check_output()
-
-#         if anat_valid_outputs:
-#             dmri_valid_inputs, dmri_pipeline = cmp.project.init_dmri_project(project, bids_layout, False)
-#             if dmri_pipeline is not None:
-#                 dmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
-#                 dmri_pipeline.atlas_info = anat_pipeline.atlas_info
-#                 # print sys.argv[offset+7]
-#                 if dmri_valid_inputs and sys.argv[offset+7]=='True':
-#                     print(">> Process diffusion pipeline")
-#                     dmri_pipeline.process()
-#                 else:
-#                     print("WARNING: Diffusion pipeline set to not be executed")
-
-#             fmri_valid_inputs, fmri_pipeline = cmp.project.init_fmri_project(project, bids_layout, False)
-#             if fmri_pipeline is not None:
-#                 fmri_pipeline.parcellation_scheme = anat_pipeline.parcellation_scheme
-#                 fmri_pipeline.atlas_info = anat_pipeline.atlas_info
-#                 # print sys.argv[offset+9]
-#                 if fmri_valid_inputs and sys.argv[offset+9]=='True':
-#                     print(">> Process fmri pipeline")
-#                     fmri_pipeline.process()
-#                 else:
-#                     print("WARNING: Diffusion pipeline set to not be executed")
-#         else:
-#             print(msg)
-#             sys.exit(1)
-
-#     else:
-#         usage()
-#         sys.exit(2)
\ No newline at end of file
diff --git a/ubuntu16.04/environment.yml b/ubuntu16.04/environment.yml
index c074e8350..08f24c030 100644
--- a/ubuntu16.04/environment.yml
+++ b/ubuntu16.04/environment.yml
@@ -5,45 +5,47 @@ channels:
 - conda-forge
 - aramislab
 - defaults
+- mrtrix3
 
 dependencies:
 - python=3.7
 - pip=20.1.1
-- ants=2.2.0
-- numpy=1.18.5
-- matplotlib=3.2.2 #2.2.3
+- ants=2.2.0  #
+- numpy=1.19.2
+- matplotlib=3.2.2  # 2.2.3
 - graphviz=2.40.1
 - traits=6.0.0
 - configparser=5.0.0
-- nipype=1.5.0
+- nipype=1.5.1
 - pyside2=5.9.0a1
-- git-annex=8.20200617 #7.20190219
+- git-annex=8.20200617  # 7.20190219
 - pydotplus=2.0.2
-- dipy=1.1.0
-- cvxpy-base=1.1.5
-- cvxpy=1.1.5
+- dipy=1.3.0
+- cvxpy-base=1.1.7
+- cvxpy=1.1.7
 - obspy=1.2.2
-#- fury=0.5.1 #0.1.4 in pip/ vtk=7.0.0 in dependencies (should come with vtk 8.2.0 for dipy viz)
-#- libnetcdf=4.7.3
+- mrtrix3=3.0.2
+# - fury=0.5.1  # 0.1.4 in pip/ vtk=7.0.0 in dependencies (should come with vtk 8.2.0 for dipy viz)
+# - libnetcdf=4.7.3
 
 - pip:
     # - git+https://github.com/LTS5/cfflib.git
     - coverage==5.2
-    - duecredit==0.8.0 #0.7.0
-    #- dipy==1.1.1 #0.15.0
-    - mne==0.20.7 #0.17.1
-    # - obspy==1.2.1 #1.1.1
-    - datalad[full]==0.13.0 #0.11.3
+    - duecredit==0.8.0  # 0.7.0
+    # - dipy==1.1.1  # 0.15.0
+    - mne==0.20.7  # 0.17.1
+    # - obspy==1.2.1  # 1.1.1
+    - datalad[full]==0.13.0  # 0.11.3
     - datalad-revolution==0.6.0
     - datalad-container==0.3.1
     - datalad_neuroimaging==0.2.0
-    - pybids==0.10.2 #0.9.1
+    - pybids==0.10.2  # 0.9.1
     - apptools==4.5.0
-    - statsmodels==0.11.1 #0.9.0
-    - networkx==2.2
-    - sphinx==3.1.1 #1.5.1
-    - sphinx_rtd_theme==0.5.0 #0.4.3
+    - statsmodels==0.11.1  # 0.9.0
+    - networkx==2.4
+    - sphinx==3.1.1  # 1.5.1
+    - sphinx_rtd_theme==0.5.0  # 0.4.3
     - sphinx-argparse==0.2.5
-    - recommonmark==0.6.0 #0.5.0
-    - pydicom==2.0.0 #1.4.2
-    #- fury==0.5.0
+    - recommonmark==0.6.0  # 0.5.0
+    - pydicom==2.0.0  # 1.4.2
+    # - fury==0.5.0


Test patch:
diff --git a/.circleci/tests/configuration_files/ref_diffusion_config_5.ini b/.circleci/tests/configuration_files/ref_diffusion_config_5.ini
new file mode 100644
index 000000000..5ab29812a
--- /dev/null
+++ b/.circleci/tests/configuration_files/ref_diffusion_config_5.ini
@@ -0,0 +1,142 @@
+[Global]
+process_type = diffusion
+diffusion_imaging_model = DTI
+subjects = ['sub-01']
+subject = sub-01
+subject_session = ses-01
+modalities = []
+dmri_bids_acq = DSI
+
+[preprocessing_stage]
+total_readout = 0.0
+description = description
+denoising = True
+denoising_algo = MRtrix (MP-PCA)
+dipy_noise_model = Rician
+bias_field_correction = True
+bias_field_algo = ANTS N4
+eddy_current_and_motion_correction = True
+eddy_correction_algo = FSL eddy_correct
+eddy_correct_motion_correction = True
+partial_volume_estimation = True
+fast_use_priors = True
+resampling = (1, 1, 1)
+interpolation = interpolate
+
+[registration_stage]
+pipeline = Diffusion
+registration_mode = FSL
+diffusion_imaging_model = 
+use_float_precision = False
+ants_interpolation = BSpline
+ants_bspline_interpolation_parameters = (3,)
+ants_gauss_interpolation_parameters = (5.0, 5.0)
+ants_multilab_interpolation_parameters = (5.0, 5.0)
+ants_lower_quantile = 0.005
+ants_upper_quantile = 0.995
+ants_convergence_thresh = 1e-06
+ants_convergence_winsize = 10
+ants_linear_gradient_step = 0.1
+ants_linear_cost = MI
+ants_linear_sampling_perc = 0.25
+ants_linear_sampling_strategy = Regular
+ants_perform_syn = True
+ants_nonlinear_gradient_step = 0.1
+ants_nonlinear_cost = CC
+ants_nonlinear_update_field_variance = 3.0
+ants_nonlinear_total_field_variance = 0.0
+flirt_args = 
+uses_qform = True
+dof = 6
+fsl_cost = normmi
+no_search = True
+init = header
+contrast_type = dti
+apply_to_eroded_wm = True
+apply_to_eroded_csf = True
+apply_to_eroded_brain = False
+
+[diffusion_stage]
+diffusion_imaging_model_editor = ['DSI', 'DTI', 'HARDI']
+diffusion_imaging_model = DSI
+dilate_rois = True
+dilation_kernel = Box
+dilation_radius = 1
+recon_processing_tool_editor = ['Dipy', 'Custom']
+tracking_processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
+processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
+recon_processing_tool = Dipy
+tracking_processing_tool = MRtrix
+custom_track_file = .
+dipy_recon_config.flip_table_axis = []
+dipy_recon_config.imaging_model = DSI
+dipy_recon_config.local_model_editor = {False: '1:Tensor', True: '2:Constrained Spherical Deconvolution'}
+dipy_recon_config.local_model = True
+dipy_recon_config.lmax_order = 2
+dipy_recon_config.single_fib_thr = 0.7
+dipy_recon_config.recon_mode = Probabilistic
+dipy_recon_config.mapmri = False
+dipy_recon_config.tracking_processing_tool = MRtrix
+dipy_recon_config.laplacian_regularization = False
+dipy_recon_config.laplacian_weighting = 0.05
+dipy_recon_config.positivity_constraint = True
+dipy_recon_config.radial_order = 4
+dipy_recon_config.small_delta = 0.02
+dipy_recon_config.big_delta = 0.5
+dipy_recon_config.radial_order_values = [2, 4, 6, 8, 10, 12]
+dipy_recon_config.shore_radial_order = 4
+dipy_recon_config.shore_zeta = 700
+dipy_recon_config.shore_lambda_n = 1e-08
+dipy_recon_config.shore_lambda_l = 1e-08
+dipy_recon_config.shore_tau = 0.0441759
+dipy_recon_config.shore_constrain_e0 = False
+dipy_recon_config.shore_positive_constraint = True
+mrtrix_recon_config.flip_table_axis = []
+mrtrix_recon_config.local_model_editor = {True: 'Constrained Spherical Deconvolution'}
+mrtrix_recon_config.local_model = True
+mrtrix_recon_config.lmax_order = 2
+mrtrix_recon_config.normalize_to_b0 = False
+mrtrix_recon_config.single_fib_thr = 0.7
+mrtrix_recon_config.recon_mode = Probabilistic
+mrtrix_recon_config.imaging_model = DSI
+dipy_tracking_config.imaging_model = DSI
+dipy_tracking_config.tracking_mode = Deterministic
+dipy_tracking_config.sd = True
+dipy_tracking_config.number_of_seeds = 1000
+dipy_tracking_config.seed_density = 1.0
+dipy_tracking_config.fa_thresh = 0.2
+dipy_tracking_config.step_size = 0.5
+dipy_tracking_config.max_angle = 25.0
+dipy_tracking_config.sh_order = 8
+dipy_tracking_config.use_act = False
+dipy_tracking_config.seed_from_gmwmi = False
+dipy_tracking_config.curvature = 0.0
+mrtrix_tracking_config.tracking_mode = Deterministic
+mrtrix_tracking_config.sd = True
+mrtrix_tracking_config.desired_number_of_tracks = 200000
+mrtrix_tracking_config.curvature = 0.0
+mrtrix_tracking_config.step_size = 0.5
+mrtrix_tracking_config.min_length = 5.0
+mrtrix_tracking_config.max_length = 200.0
+mrtrix_tracking_config.angle = 45.0
+mrtrix_tracking_config.cutoff_value = 0.05
+mrtrix_tracking_config.use_act = False
+mrtrix_tracking_config.seed_from_gmwmi = False
+mrtrix_tracking_config.crop_at_gmwmi = False
+mrtrix_tracking_config.backtrack = False
+mrtrix_tracking_config.sift = True
+diffusion_model_editor = ['Deterministic', 'Probabilistic']
+diffusion_model = Deterministic
+
+[connectome_stage]
+output_types = ['gPickle']
+connectivity_metrics = ['Fiber number', 'Fiber length', 'Fiber density', 'Fiber proportion', 'Normalized fiber density', 'ADC', 'gFA']
+probtrackx = False
+compute_curvature = False
+log_visualization = True
+circular_layout = False
+subject = 
+
+[Multi-processing]
+number_of_cores = 1
+
diff --git a/.circleci/tests/configuration_files/ref_fMRI_config_2.ini b/.circleci/tests/configuration_files/ref_fMRI_config_2.ini
new file mode 100644
index 000000000..d984debb1
--- /dev/null
+++ b/.circleci/tests/configuration_files/ref_fMRI_config_2.ini
@@ -0,0 +1,72 @@
+[Global]
+process_type = fMRI
+imaging_model = 
+subjects = ['sub-01']
+subject = sub-01
+subject_session = ses-01
+
+[preprocessing_stage]
+discard_n_volumes = 5
+despiking = True
+slice_timing = bottom-top interleaved
+repetition_time = 0.5
+motion_correction = True
+
+[registration_stage]
+ants_convergence_winsize = 10
+ants_nonlinear_update_field_variance = 3.0
+flirt_args =
+contrast_type = dti
+ants_upper_quantile = 0.995
+use_float_precision = False
+ants_nonlinear_total_field_variance = 0.0
+registration_mode = FSL (Linear)
+init = header
+ants_interpolation = Linear
+ants_linear_sampling_perc = 0.25
+apply_to_eroded_wm = True
+ants_convergence_thresh = 1e-06
+ants_multilab_interpolation_parameters = (5.0, 5.0)
+ants_gauss_interpolation_parameters = (5.0, 5.0)
+ants_nonlinear_cost = CC
+ants_bspline_interpolation_parameters = (3,)
+apply_to_eroded_brain = False
+uses_qform = True
+pipeline = fMRI
+ants_lower_quantile = 0.005
+no_search = True
+ants_linear_cost = MI
+ants_linear_gradient_step = 0.1
+apply_to_eroded_csf = True
+ants_perform_syn = True
+ants_linear_sampling_strategy = Regular
+dof = 6
+diffusion_imaging_model =
+fsl_cost = normmi
+ants_nonlinear_gradient_step = 0.1
+
+[functional_stage]
+smoothing = 0.0
+discard_n_volumes = 5
+global_nuisance = True
+csf = True
+wm = True
+motion = True
+detrending = True
+detrending_mode = linear
+lowpass_filter = 0.01
+highpass_filter = 0.1
+scrubbing = True
+
+[connectome_stage]
+output_types = ['gPickle', 'mat']
+apply_scrubbing = True
+fd_thr = 0.2
+dvars_thr = 4.0
+log_visualization = True
+circular_layout = False
+subject = sub-01
+
+[Multi-processing]
+number_of_cores = 1
+
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt
new file mode 100644
index 000000000..79f924ece
--- /dev/null
+++ b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt
@@ -0,0 +1,1067 @@
+cmp/dataset_description.json
+cmp/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
+cmp/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale1_atlas_FreeSurferColorLUT.txt
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale1_atlas.graphml
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale1_atlas.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale1_stats.tsv
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale2_atlas_flirt.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale2_atlas_FreeSurferColorLUT.txt
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale2_atlas.graphml
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale2_atlas.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale2_stats.tsv
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale3_atlas_flirt.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale3_atlas_FreeSurferColorLUT.txt
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale3_atlas.graphml
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale3_atlas.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale3_stats.tsv
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale4_atlas_flirt.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale4_atlas_FreeSurferColorLUT.txt
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale4_atlas.graphml
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale4_atlas.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale4_stats.tsv
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale5_atlas_flirt.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale5_atlas_FreeSurferColorLUT.txt
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale5_atlas.graphml
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale5_atlas.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-L2018_desc-scale5_stats.tsv
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz
+cmp/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-WM_dseg.nii.gz
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+cmp/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz
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