[MAINT] remove freesurfer from Dockerfile (#106)

* remove freesurfer from Dockerfile

* bump the version for the docker cache

* remove check for freesurfer

Author: jdkent

.circleci/config.yml

@@ -12,10 +12,10 @@ jobs:
             apk add --no-cache pigz python3
       - restore_cache:
           keys:
-            - docker-v1-{{ .Branch }}-{{ epoch }}
-            - docker-v1-{{ .Branch }}-
-            - docker-v1-master-
-            - docker-v1-
+            - docker-v2-{{ .Branch }}-{{ epoch }}
+            - docker-v2-{{ .Branch }}-
+            - docker-v2-master-
+            - docker-v2-
           paths:
             - /tmp/cache/docker.tar.gz
       - checkout
@@ -56,7 +56,7 @@ jobs:
             - cache/docker.tar.gz
             - src/RestingState
       - save_cache:
-          key: docker-v1-{{ .Branch }}-{{ epoch }}
+          key: docker-v2-{{ .Branch }}-{{ epoch }}
           paths:
             - /tmp/cache/docker.tar.gz
 

Dockerfile

@@ -36,27 +36,6 @@ RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
     fsl \
     fsl-atlases
 
-# 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'
-
 # Installing and setting up miniconda
 RUN curl -sSLO https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
     bash Miniconda2-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
@@ -99,19 +78,8 @@ ENV FSLDIR=/usr/share/fsl/5.0 \
     LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
     FSLTCLSH=/usr/bin/tclsh \
     FSLWISH=/usr/bin/wish \
-    FSF_OUTPUT_FORMAT="nii.gz" \
-    FREESURFER_HOME="/opt/freesurfer" \
     PATH="/opt/ICA-AROMA:/opt/RestingState:/usr/lib/afni/bin/:/usr/lib/fsl/5.0:$PATH"
 
-ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
-    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
-    MNI_DIR="$FREESURFER_HOME/mni" \
-    LOCAL_DIR="$FREESURFER_HOME/local" \
-    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
-    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
-    MNI_DATAPATH="$FREESURFER_HOME/mni/data" \
-    PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$PATH"
-
 # clean up
 RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 

processRestingState_bids_wrapper.sh

@@ -52,12 +52,6 @@ function softwareCheck()
       echo "fsl is either not downloaded or not defined in your path, exiting script"
       exit 1
   fi
-
-  if [ "$(which freesurfer)" == "" ]; then
-      echo "freesurfer is either not downloaded or not defined in your path, exiting script"
-      exit 1
-  fi
-
 }
 
 function clobber()