Merge pull request #2779 from effigies/docker/22.0.0-fs7

DOCKER: Bundle FreeSurfer 7
nipreps · May 20, 2022 · 26d7fae · 26d7fae
2 parents a320ec6 + e144b75
commit 26d7fae
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diff --git a/Dockerfile b/Dockerfile
@@ -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" \
@@ -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 \
@@ -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