Adding FreeSurfer commands (for validation tests)

Docker/Dockerfile

@@ -114,9 +114,9 @@ SHELL ["/bin/bash", "--login", "-c"]
 
 # install freesurfer and point to new python location
 RUN /install/install_fs_pruned.sh /opt --upx && \
-    rm /opt/freesurfer/bin/fspython &&  \
-    rm -R /install && \
-    ln -s /venv/bin/python3 /opt/freesurfer/bin/fspython
+rm /opt/freesurfer/bin/fspython &&  \
+rm -R /install && \
+ln -s /venv/bin/python3 /opt/freesurfer/bin/fspython
 
 
 # =======================================================
@@ -175,7 +175,7 @@ COPY /Docker/python-s /venv/bin/
 
 # Copy fastsurfer over from the build context and add PYTHONPATH
 COPY . /fastsurfer/
-ENV PYTHONPATH=/fastsurfer:$PYTHONPATH \
+ENV PYTHONPATH=/fastsurfer:/opt/freesurfer/python/package:$PYTHONPATH \
     FASTSURFER_HOME=/fastsurfer
 
 # Download all remote network checkpoints already, compile all FastSurfer scripts into bytecode and update

Docker/install_fs_pruned.sh

@@ -80,7 +80,6 @@ wget --no-check-certificate -qO- $fslink  | tar zxv --no-same-owner -C $where \
       --exclude='freesurfer/python/bin' \
       --exclude='freesurfer/python/include' \
       --exclude='freesurfer/python/lib' \
-      --exclude='freesurfer/python/packages' \
       --exclude='freesurfer/python/share' \
       --exclude='freesurfer/subjects/bert' \
       --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
@@ -106,6 +105,7 @@ mkdir -p $fsd/bin
 mkdir -p $fsd/etc
 mkdir -p $fsd/lib/bem
 mkdir -p $fsd/python/scripts
+mkdir -p $fsd/python/packages/fsbindings
 mkdir -p $fsd/subjects/fsaverage/label
 mkdir -p $fsd/subjects/fsaverage/surf
 
@@ -146,15 +146,21 @@ copy_files="
   average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
   bin/analyzeto4dfp
   bin/AntsDenoiseImageFs
+  bin/asegstats2table
+  bin/aparcstats2table
   bin/avi2talxfm
   bin/compute_vox2vox
   bin/defect2seg
+  bin/fname2stem
+  bin/fspython
   bin/fs_temp_dir
   bin/fs_temp_file
   bin/fs-check-version
   bin/fsr-getxopts
   bin/gauss_4dfp
   bin/imgreg_4dfp
+  bin/isanalyze
+  bin/isnifti
   bin/lta_convert
   bin/mpr2mni305
   bin/mri_add_xform_to_header
@@ -169,6 +175,7 @@ copy_files="
   bin/mri_edit_wm_with_aseg
   bin/mri_fill
   bin/mri_fuse_segmentations
+  bin/mri_glmfit
   bin/mri_info
   bin/mri_label2label
   bin/mri_label2vol
@@ -182,6 +189,7 @@ copy_files="
   bin/mri_robust_template
   bin/mri_segment
   bin/mri_segstats
+  bin/mri_surf2surf
   bin/mri_surf2volseg
   bin/mri_tessellate
   bin/mri_vol2surf
@@ -203,6 +211,7 @@ copy_files="
   bin/mris_jacobian
   bin/mris_label2annot
   bin/mris_place_surface
+  bin/mris_preproc
   bin/mris_register
   bin/mris_remesh
   bin/mris_remove_intersection
@@ -222,6 +231,9 @@ copy_files="
   etc/recon-config.yaml
   lib/bem/ic4.tri
   lib/bem/ic7.tri
+  python/packages/fsbindings/legacy.py
+  python/scripts/asegstats2table
+  python/scripts/aparcstats2table
   python/scripts/rca-config
   python/scripts/rca-config2csh
   subjects/fsaverage/label/lh.aparc.annot
@@ -308,9 +320,11 @@ echo
 for file in $copy_files
 do
   echo "copying $file"
-  cp $fss/$file $fsd/$file
+  cp -r $fss/$file $fsd/$file
 done
 
+# Modify fsbindings Python package to allow calling scripts like asegstats2table directly:
+echo "from . import legacy" > "$fsd/python/packages/fsbindings/__init__.py"
 
 # FS looks for them, but does not call them
 touch_files="/average/RB_all_2020-01-02.gca"
@@ -341,7 +355,6 @@ link_files="
   bin/mri_relabel_nonwm_hypos
   bin/mri_remove_neck
   bin/mri_stats2seg
-  bin/mri_surf2surf
   bin/mri_surf2vol
   bin/mri_surfcluster
   bin/mri_vol2vol