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FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh) #404

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merged 4 commits into from
Dec 7, 2023
Merged

FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh) #404

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741345d
add missing dependency of FreeSurfer
psadil Nov 29, 2023
707c429
remove file from FS derivatives to ensure part of recon-all runs
psadil Nov 30, 2023
8c98204
replace removal wmparc.stats with lh.aparc.stats
psadil Nov 30, 2023
13cacd8
replace autorecon3,autorecon-hemi attempt with cortribbon
psadil Nov 30, 2023
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3 changes: 3 additions & 0 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -458,6 +458,9 @@ jobs:
name: Run anatomical workflow on ds005
no_output_timeout: 2h
command: |
# Remove part of FreeSurfer output to ensure that at least
# some of recon-all is attempted
rm /tmp/ds005/freesurfer/sub-01/mri/ribbon.mgz
bash /tmp/src/smriprep/.circleci/ds005_run.sh --write-graph
- run:
name: Combine coverage
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3 changes: 2 additions & 1 deletion Dockerfile
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Expand Up @@ -93,7 +93,7 @@ ENV DEBIAN_FRONTEND="noninteractive" \
LC_ALL="en_US.UTF-8"

# Some baseline tools
# bc is needed for FreeSurfer
# bc, tcsh are needed for FreeSurfer
# libglu1-mesa is needed for Connectome Workbench
RUN apt-get update && \
apt-get install -y --no-install-recommends \
Expand All @@ -105,6 +105,7 @@ RUN apt-get update && \
libglu1-mesa \
lsb-release \
netbase \
tcsh \
xvfb && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

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