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DOCKER: Bundle FreeSurfer 7 #2779

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merged 9 commits into from
May 20, 2022
Merged

DOCKER: Bundle FreeSurfer 7 #2779

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f85abcb
DOCKER: Add FS7 exclusion file
effigies Sep 22, 2021
e63937c
DOCKER: Consolidate exclusions to untouched files/directories
effigies Sep 22, 2021
ce036fe
DOCKER: Preserve fsaverage{,5,6}, mris_expand
effigies Sep 22, 2021
a9f7103
DOCKER: Keep licenses in docs/ directory
effigies Sep 22, 2021
0fc3601
DOCKER: Preserve bbregister and subcommands
effigies Sep 22, 2021
aafda62
DOCKER: Bundle FreeSurfer 7.2.0
effigies May 17, 2022
c6e3d28
DOCKER: Restore tools needed by recon-all
effigies May 18, 2022
4800211
DOCKER: Add hack for recon-all bug
effigies May 19, 2022
e144b75
MNT: Require recent nipype with FS 7 support
effigies May 19, 2022
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29 changes: 8 additions & 21 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -48,26 +48,9 @@ ENV DEBIAN_FRONTEND="noninteractive" \
LC_ALL="en_US.UTF-8"

# Installing freesurfer
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz \
| tar zxv --no-same-owner -C /opt \
--exclude='freesurfer/diffusion' \
--exclude='freesurfer/docs' \
--exclude='freesurfer/fsfast' \
--exclude='freesurfer/lib/cuda' \
--exclude='freesurfer/lib/qt' \
--exclude='freesurfer/matlab' \
--exclude='freesurfer/mni/share/man' \
--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/subjects/fsaverage3' \
--exclude='freesurfer/subjects/fsaverage4' \
--exclude='freesurfer/subjects/cvs_avg35' \
--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
--exclude='freesurfer/subjects/bert' \
--exclude='freesurfer/subjects/lh.EC_average' \
--exclude='freesurfer/subjects/rh.EC_average' \
--exclude='freesurfer/subjects/sample-*.mgz' \
--exclude='freesurfer/subjects/V1_average' \
--exclude='freesurfer/trctrain'
COPY docker/files/freesurfer7.2-exclude.txt /usr/local/etc/freesurfer7.2-exclude.txt
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz \
 | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.2-exclude.txt

# Simulate SetUpFreeSurfer.sh
ENV FSL_DIR="/opt/fsl-6.0.5.1" \
Expand All @@ -85,7 +68,7 @@ ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
MNI_DATAPATH="$FREESURFER_HOME/mni/data"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"

# FSL 6.0.5.1
RUN apt-get update -qq \
Expand Down Expand Up @@ -311,6 +294,10 @@ RUN find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} + && \
rm -rf $HOME/.npm $HOME/.conda $HOME/.empty

# HACK for FreeSurfer 7.2.0
# Fixed in https://github.com/freesurfer/freesurfer/pull/886, so remove on release
ENV FREESURFER="/opt/freesurfer"

ENV IS_DOCKER_8395080871=1

RUN ldconfig
Expand Down
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