From a1804f005bea9630c338b4bdc5896aad6f9462f2 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Wed, 2 Oct 2024 15:12:02 -0400
Subject: [PATCH] Remove Freesurfer (#28)

* Remove Freesurfer.

* Change connectome-workbench version.
---
 Dockerfile | 36 ------------------------------------
 1 file changed, 36 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ee0be23..e14b9ec 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -161,42 +161,6 @@ ENV FSLDIR="/opt/fsl" \
     PATH="/opt/fsl/lib:/opt/fsl/bin:$PATH" \
     FSL_DEPS="libquadmath0;libnewimage.so;libmiscmaths.so"
 
-# Install 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"
-
-ENV FREESURFER_HOME="/opt/freesurfer" \
-    FSF_OUTPUT_FORMAT="nii.gz"
-
-ENV FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
-    LOCAL_DIR="$FREESURFER_HOME/local" \
-    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
-    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
-    MNI_DIR="$FREESURFER_HOME/mni" \
-    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
-
-ENV MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
-    SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
-    PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
-
 # Install ANTS
 ENV ANTSPATH="/usr/lib/ants"
 RUN mkdir -p $ANTSPATH && \