Repository: connectomicslab/connectomemapper3 (language: python)

Issue:
BUG: Running `cmpbidsappmanager` just hangs, no GUI appearing
_Issue related to JOSS review: https://github.com/openjournals/joss-reviews/issues/4248_

When running `cmpbidsappmanager`, the following appears in the terminal:

```
>> cmpbidsappmanager

Connectome Mapper v3.0.3 - BIDS App Manager
------------------------------------------------------
Copyright (C) 2009-2022, Ecole Polytechnique Federale de Lausanne (EPFL) the University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland, and Contributors, All rights reserved.
------------------------------------------------------
------------------------------------------------------
  .. INFO: Use qt for graphical backend
------------------------------------------------------

_
```

then an icon appears in my Mac's doc bar:

<img width="113" alt="Screenshot 2022-04-15 at 12 25 38" src="https://user-images.githubusercontent.com/10141237/163560673-4fa7d2eb-f492-4524-ab0a-d5a7aed9a7fb.png">

and after that nothing happens. Have tried multiple times, no difference. I'm expecting the GUI to appear, is that what should happen? Should I do something about the note regarding `qt`?



DOC: Add size of docker image to docs
_Issue related to JOSS review: https://github.com/openjournals/joss-reviews/issues/4248_

It could be useful to add a sentence to the Installation instructions that mention the size of the docker image that will be pulled, so that users know what to expect (6.27GB compressed for v3.0.3, according to https://hub.docker.com/r/sebastientourbier/connectomemapper-bidsapp/tags)


Discussion / hints:
Hi @jsheunis,

Sorry to hear you are still having issues with the GUI...

This is indeed not the expected behaviour and a window should appear at this point.

I tried to reproduce it on my macbookpro (MacOS Catalina 10.15.7 / conda 4.11.0) (I completely uninstalled connectomemapper3 and the environment and I reinstalled it following the instructions in the docs and the workaround in #160 ), but it appears `cmpbidsappmanager` starts without any problem on my machine.

**Possible source of problem**
This made me suspecting that it might be related to Qt-based GUI on Big Sur and after searching on internet, I discovered that several Qt-based applications had a similar issue when using PyQt/PySide2 >= 5.13.2 and < 5.15.2:
- https://stackoverflow.com/questions/64833558/apps-not-popping-up-on-macos-big-sur-11-0-1
- https://bugreports.qt.io/browse/QTBUG-87014
- https://stackoverflow.com/questions/64818879/is-there-any-solution-regarding-to-pyqt-library-doesnt-work-in-mac-os-big-sur/64856281
- https://keremkoseoglu.wordpress.com/2020/11/14/pyqt5-problem-on-macos-big-sur-solved/
- https://tickets.metabrainz.org/browse/PICARD-1858

In our case, PyQt/PySide2 5.13.2 is indeed installed in our `py37cmp-gui` environment:
https://github.com/connectomicslab/connectomemapper3/blob/bb40f8e78020814579da3ea8fc29e63437ad238c/conda/environment_macosx.yml#L19

In this sense, the closest issue would correspond to the last enumerated one (https://tickets.metabrainz.org/browse/PICARD-1858) that was fixed here: https://github.com/metabrainz/picard/pull/1633#issue-708781859. Briefly, it consisted in downgrading PyQt from 5.13.2 to 5.13.1.

**Possible solution**
Please could you try to modify the `environment_macosx.yml` by changing the line ` - pyside2=5.13.2` to  `- pyside2=5.13.1` and reinstall the environment as follows?
```bash
conda deactivate # make sure the py37cmp-gui environment is not activated
conda env remove -n py37cmp-gui
conda env create -f /path/to/edited/environment_macosx.yml
```

As regards

> Should I do something about the note regarding qt?

I would say here no.

The tool used for graphical backend of the TraitsUI elements, which is selected by setting the environment variables `ETS_TOOLKIT` and `QT_API`:

https://github.com/connectomicslab/connectomemapper3/blob/bb40f8e78020814579da3ea8fc29e63437ad238c/cmp/cli/cmpbidsappmanager.py#L14-L16

and the message `INFO: Use qt for graphical backend` is just used to confirm that `ETS_TOOLKIT` has been set to `qt`:

https://github.com/connectomicslab/connectomemapper3/blob/bb40f8e78020814579da3ea8fc29e63437ad238c/cmp/cli/cmpbidsappmanager.py#L31

Let me know if this works or if you have any further questions.

Best
I did as you suggested, but still had the same issue.

After removing the existing conda environment, and installing a new one from the edited `environment_macosx.yml` file, I ran `pip list`. This included the following:

```
PyQt5                         5.12.3
PyQt5_sip                     4.19.18
PyQtChart                     5.12
PyQtWebEngine                 5.12.1
```

I'm not deeply familiar with the connection between `pyside2` and `PyQt`, but I'm guessing after setting `pyside2=5.12.1` in the environment file, we'd want `PyQt5` to have the same version number? If so, this doesn't seem to be happening during the conda environment creation.

I tried uninstalling `PyQt5` and reinstalling it with the specific version:

```
pip uninstall PyQt5
pip install PyQt5==5.12.1
pip list
>>
PyQt5                         5.12.1
PyQt5_sip                     4.19.18
PyQtChart                     5.12
PyQtWebEngine                 5.12.1
```

which executed successfully, but the initial issue still remained. Any other ideas?

If this persists, I'm not sure that this issue should necessarily hold up the JOSS review if it's just an edge case.
That's what I would have also done...

Another idea could be to update PyQt5 to the latest version (as it seems it was fixed in version >= 5.15.2), and choose pyqt5 as backend directly.

1. To reinstall the latest version of PyQt5:
```
$ pip uninstall PyQt5
$ pip install PyQt5==5.15.6
```

2. To choos PyQt5 directly, you would need to uncomment line 15 and comment line 16 in the file `cmpbidsappmanager.py`:
    
   https://github.com/connectomicslab/connectomemapper3/blob/bb40f8e78020814579da3ea8fc29e63437ad238c/cmp/cli/cmpbidsappmanager.py#L14-L16

    that should be found in the `.../miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/cli` folder. This will tell `traitsui` to use directly PyQt5 as backend.

Hope this will work 🤞 


Perhaps the expected time it will take to download could also be useful? Or just a note that this process might take some time. It took around 40min to pull the image on my Macbook pro with a decent internet connection speed.

Likelwise, creating the conda environment also took very long.



Fix patch:
diff --git a/.circleci/config.yml b/.circleci/config.yml
index 92f0d2a21..7f4fd0b68 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -401,6 +401,7 @@ jobs:
       - run:
           name: Enable "--squash" feature of docker build
           command: |
+            # Enable the --squash feature
             sudo touch /etc/docker/daemon.json
             echo "{\"experimental\": true}" | sudo tee -a /etc/docker/daemon.json
             sudo service docker restart
@@ -442,8 +443,13 @@ jobs:
             fi
             # Build CMP BIDS App docker image
             cd /home/circleci/src/connectomemapper3
-            ls -la .
-            DOCKER_BUILDKIT=1 docker build --progress=plain --squash --rm=true --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" -t sebastientourbier/connectomemapper3 /home/circleci/src/connectomemapper3 \
+            export DOCKER_BUILDKIT=1
+            docker build --progress=plain \
+              --squash --rm=true \
+              --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
+              --build-arg VCS_REF=`git rev-parse --short HEAD` \
+              --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" \
+              -t sebastientourbier/connectomemapper3 /home/circleci/src/connectomemapper3
       #- run:
       #    name: Prune Docker cache (temporary)
       #    command: docker system prune -f
diff --git a/cmp/info.py b/cmp/info.py
index 664955c78..a811eab24 100644
--- a/cmp/info.py
+++ b/cmp/info.py
@@ -7,9 +7,9 @@
 
 _version_major = 3
 _version_minor = 0
-_version_micro = 3
+_version_micro = 4
 _version_extra = ""
-__release_date__ = "21.02.2022"
+__release_date__ = "15.06.2022"
 
 __minor_version__ = "%s.%s" % (_version_major, _version_minor)
 
diff --git a/docker/environment.yml b/docker/environment.yml
index ce26b2361..da1c8be9b 100644
--- a/docker/environment.yml
+++ b/docker/environment.yml
@@ -14,8 +14,7 @@ dependencies:
 - graphviz=2.40.1
 - traits=6.2.0
 - configparser=5.0.0
-- nipype=1.7.0
-- pyside2=5.9.0a1
+- nipype=1.8.0
 - git-annex=8.20200617
 - pydotplus=2.0.2
 - dipy=1.3.0
@@ -27,12 +26,12 @@ dependencies:
 - pip:
     - coverage==5.2
     - duecredit==0.8.0
-    - mne==0.20.7
-    - datalad[full]==0.14.0
-    - datalad-container==1.1.2
-    - datalad_neuroimaging==0.3.1
+    - mne==0.24.1
+    - datalad[full]==0.15.4
+    - datalad-container==1.1.5
+    - datalad-neuroimaging==0.3.1
     - pybids==0.14.0
     - statsmodels==0.11.1
-    - networkx==2.4
-    - pydicom==2.0.0
+    - networkx==2.6.3
+    - pydicom==2.2.2
     - pycartool==0.1.1
diff --git a/docker/requirements.txt b/docker/requirements.txt
index 87d5ecd1d..e151ded88 100644
--- a/docker/requirements.txt
+++ b/docker/requirements.txt
@@ -1,12 +1,12 @@
 coverage==5.2
 duecredit==0.8.0
-mne==0.20.7
-datalad[full]==0.14.0
-datalad-container==1.1.2
-datalad_neuroimaging==0.3.1
+mne==0.24.1
+datalad[full]==0.15.4
+datalad-container==1.1.5
+datalad-neuroimaging==0.3.1
 pybids==0.14.0
-statsmodels==0.11.1
-networkx==2.4
-pydicom==2.0.0
+statsmodels==0.13.1
+networkx==2.6.3
+pydicom==2.2.2
 scikit-image==0.16.2
 pycartool==0.1.1
diff --git a/docker/spec-file.txt b/docker/spec-file.txt
index 184d3cdc1..55b8318f0 100644
--- a/docker/spec-file.txt
+++ b/docker/spec-file.txt
@@ -249,7 +249,6 @@ https://conda.anaconda.org/conda-forge/linux-64/vtk-9.0.1-no_osmesa_py37h111716f
 https://conda.anaconda.org/conda-forge/linux-64/graphviz-2.40.1-h0511662_2.tar.bz2
 https://conda.anaconda.org/mrtrix3/linux-64/mrtrix3-3.0.2-h6bb024c_0.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/osqp-0.6.2.post0-py37he8f5f7f_3.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/pyside2-5.9.0a1-py37h4dc837a_0.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/statsmodels-0.13.1-py37hb1e94ed_0.tar.bz2
 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.7-pyhd8ed1ab_0.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/cvxpy-1.1.7-py37h89c1867_1.tar.bz2
@@ -261,6 +260,5 @@ https://conda.anaconda.org/conda-forge/linux-64/obspy-1.2.2-py37hb1e94ed_2.tar.b
 https://conda.anaconda.org/conda-forge/noarch/pooch-1.5.2-pyhd8ed1ab_0.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/rdflib-6.0.2-py37h89c1867_0.tar.bz2
 https://conda.anaconda.org/conda-forge/noarch/prov-2.0.0-pyhd3deb0d_0.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.18.3-py37he8f5f7f_1.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/dipy-1.3.0-py37ha21ca33_1.tar.bz2
-https://conda.anaconda.org/conda-forge/linux-64/nipype-1.7.0-py37h89c1867_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/nipype-1.8.0-py37h89c1867_0.tar.bz2
diff --git a/docs/bidsappmanager.rst b/docs/bidsappmanager.rst
index f8717a13e..459189bab 100644
--- a/docs/bidsappmanager.rst
+++ b/docs/bidsappmanager.rst
@@ -32,20 +32,20 @@ After activation of the conda environment, start the graphical user interface ca
     $ cmpbidsappmanager
 
 
+.. note:: The main window would be blank until you select the BIDS dataset.
+
 Load a BIDS dataset
 ***********************
 
-The ``Connectome Mapper 3`` BIDS App Manager allows you to:
-
-* load a BIDS dataset stored locally.
-
-You only have to select the root directory of your valid BIDS dataset (see note below)
+*   Click on `File -> Load BIDS dataset...` in the menu bar of the main window. Note that on Mac, Qt turns this menu bar into the native menu bar (top of the screen).
 
-* create a new datalad/BIDS dataset locally from an existing local or remote datalad/BIDS dataset (This is a feature under development)
+    The ``Connectome Mapper 3`` BIDS App Manager gives you two different options:
 
-Select the mode "Install a Datalad/BIDS dataset".
+    *   `Load BIDS dataset`: load a BIDS dataset stored locally.
+        You only have to select the root directory of your valid BIDS dataset (see note below)
 
-If ssh connection is used, make sure to enable the  "install via ssh" and to provide all connection details (IP address / Remote host name, remote user, remote password)
+    *   `Install Datalad BIDS dataset`: create a new datalad/BIDS dataset locally from an existing local or remote datalad/BIDS dataset (This is a feature under development)
+        If ssh connection is used, make sure to enable the  "install via ssh" and to provide all connection details (IP address / Remote host name, remote user, remote password)
 
 .. 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/>`_.
 
diff --git a/docs/changes.rst b/docs/changes.rst
index 784cf764c..44a0d7c37 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -2,6 +2,66 @@
 Changes
 ========
 
+****************************
+Version 3.0.4
+****************************
+
+Date: June 15, 2022
+
+This version mainly addresses all points raised by the JOSS review (https://github.com/openjournals/joss-reviews/issues/4248).
+
+**What's Changed**
+
+*Updates*
+
+*   Nipype has been updated from ``1.7.0`` to ``1.8.0``. (`PR #184 <https://github.com/connectomicslab/connectomemapper3/pull/184>`_)
+    See `Nipype changelog <https://nipype.readthedocs.io/en/latest/changes.html#may-10-2022>`_) for more details.
+
+*Bug fix*
+
+*   Add missing `cmp.stages.eeg` to `setup_pypi.py`. (`PR #166 <https://github.com/connectomicslab/connectomemapper3/pull/166>`_)
+
+*   Add missing package data for parcellation in `setup_pypi.py`. (`PR #182 <https://github.com/connectomicslab/connectomemapper3/pull/182>`_)
+
+*   Use HTTPS instead of SSH for datalad clone in notebooks . (`PR #181 <https://github.com/connectomicslab/connectomemapper3/pull/181>`_)
+
+*   Add missing condition to handle custom BIDS files with session. (`PR #183 <https://github.com/connectomicslab/connectomemapper3/pull/183>`_)
+
+*   Integrate fix from Napari project for issues with menubar on Mac. (`PR #174 <https://github.com/connectomicslab/connectomemapper3/pull/174>`_)
+
+*   Use the most recent PyQt5 instead of PySide2 (older) for graphical backend of `cmpbidsappmanager`, which provides a fix to run Qt-based GUI on MacOSX Big Sur. (`PR #188 <https://github.com/connectomicslab/connectomemapper3/pull/188>`_)
+
+*Documentation*
+
+*   Correct `conda env create` instruction in the README. (`PR #164 <https://github.com/connectomicslab/connectomemapper3/pull/164>`_)
+
+*   Refer to contributing guidelines in the README. (`PR #167 <https://github.com/connectomicslab/connectomemapper3/pull/167>`_)
+
+*   Use `sphinx-copybutton` extension in the docs. (`PR #168 <https://github.com/connectomicslab/connectomemapper3/pull/168>`_)
+
+*   Add notes about docker image and conda environment size and time to download. (`PR #169 <https://github.com/connectomicslab/connectomemapper3/pull/169>`_)
+
+*JOSS paper*
+
+*   Integrate minor wording tweaks by @jsheunis. (`PR #162 <https://github.com/connectomicslab/connectomemapper3/pull/162>`_)
+
+*   Add higher level summary and rename the old summary to "Overview of Functionalities". (`PR #175 <https://github.com/connectomicslab/connectomemapper3/pull/175>`_)
+
+*License*
+
+*   The license has been updated to a pure 3-clause BSD license to comply with JOSS. (`PR #163 <https://github.com/connectomicslab/connectomemapper3/pull/163>`_)
+
+*Software development life cycle*
+
+*   Migrate ubuntu 16.04 (now deprecated) to 20.04 on CircleCI. (`PR #172 <https://github.com/connectomicslab/connectomemapper3/pull/172>`_)
+
+*Contributors*
+
+*   `Sebastien Tourbier <https://github.com/connectomicslab/connectomemapper3/issues?q=is%3Apr+author%3Asebastientourbier>`_
+
+*   `J.S. (Stephan) Heunis <https://github.com/connectomicslab/connectomemapper3/issues?q=is%3Apr+author%3Ajsheunis>`_
+
+
 ****************************
 Version 3.0.3
 ****************************


Test patch:
diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt
index 430c151dd..def268643 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt
@@ -1,43 +1,43 @@
-cmp-v3.0.3/dataset_description.json
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
-cmp-v3.0.3/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
+cmp-v3.0.4/dataset_description.json
+cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml
+cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz
+cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv
+cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt
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diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt
index 3315e49c4..09c416e11 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt
@@ -1,22 +1,22 @@
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 freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab
@@ -361,44 +361,44 @@ freesurfer-7.1.1/sub-01_ses-01/touch/talairach.touch
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diff --git a/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt
index 6c81a006d..f6854f963 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt
@@ -38,44 +38,44 @@ cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
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diff --git a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt
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diff --git a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt
index 216abd1d3..3ae969bc0 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt
@@ -1,81 +1,81 @@
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diff --git a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt
index dd8687989..0b450de6a 100644
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 freesurfer-7.1.1/dataset_description.json
 freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
 freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab
@@ -433,287 +433,287 @@ freesurfer-7.1.1/sub-01_ses-01/touch/talairach.touch
 freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.stats.touch
 freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.touch
 freesurfer-7.1.1/sub-01_ses-01/touch/wmsegment.touch
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diff --git a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt
index 68429e69d..4349d1ae0 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt
@@ -1,83 +1,83 @@
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diff --git a/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt
index 430c151dd..def268643 100644
--- a/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt
+++ b/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt
@@ -1,43 +1,43 @@
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