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[RTM] Add freesurfer 6.0.0 (RC) to dockerfile #338

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Merged
merged 4 commits into from
Jan 15, 2017
Merged

[RTM] Add freesurfer 6.0.0 (RC) to dockerfile #338

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36fdb80
added freesurfer
chrisgorgo Jan 14, 2017
1d194a0
fixed path
chrisgorgo Jan 14, 2017
f31d516
switch from wget to curl
chrisgorgo Jan 15, 2017
c891285
increased timeout
chrisgorgo Jan 15, 2017
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35 changes: 35 additions & 0 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,41 @@ ENV AFNI_TTATLAS_DATASET=/usr/share/afni/atlases
ENV AFNI_PLUGINPATH=/usr/lib/afni/plugins
ENV PATH=/usr/lib/afni/bin:$PATH

# Installing freesurfer
RUN curl -sSL ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-release-candidate/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
--exclude='freesurfer/trctrain' \
--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/subjects/fsaverage3' \
--exclude='freesurfer/subjects/fsaverage4' \
--exclude='freesurfer/subjects/fsaverage5' \
--exclude='freesurfer/subjects/fsaverage6' \
--exclude='freesurfer/subjects/cvs_avg35' \
--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
--exclude='freesurfer/subjects/bert' \
--exclude='freesurfer/subjects/V1_average' \
--exclude='freesurfer/average/mult-comp-cor' \
--exclude='freesurfer/lib/cuda' \
--exclude='freesurfer/lib/qt'

ENV FSL_DIR=/usr/share/fsl/5.0
ENV OS Linux
ENV FS_OVERRIDE 0
ENV FIX_VERTEX_AREA=
ENV SUBJECTS_DIR /opt/freesurfer/subjects
ENV FSF_OUTPUT_FORMAT nii.gz
ENV MNI_DIR /opt/freesurfer/mni
ENV LOCAL_DIR /opt/freesurfer/local
ENV FREESURFER_HOME /opt/freesurfer
ENV FSFAST_HOME /opt/freesurfer/fsfast
ENV MINC_BIN_DIR /opt/freesurfer/mni/bin
ENV MINC_LIB_DIR /opt/freesurfer/mni/lib
ENV MNI_DATAPATH /opt/freesurfer/mni/data
ENV FMRI_ANALYSIS_DIR /opt/freesurfer/fsfast
ENV PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
ENV MNI_PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
ENV PATH /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:$PATH
RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh

# Installing and setting up ANTs
RUN mkdir -p /opt/ants && \
curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \
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3 changes: 2 additions & 1 deletion circle.yml
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Expand Up @@ -27,7 +27,8 @@ dependencies:

override:
- if [[ -e $HOME/docker/image.tar ]]; then docker load -i $HOME/docker/image.tar; fi
- e=1 && for i in {1..5}; do docker build -t poldracklab/fmriprep:latest --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ]
- e=1 && for i in {1..5}; do docker build -t poldracklab/fmriprep:latest --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
timeout: 21600
- mkdir -p $HOME/docker; docker save poldracklab/fmriprep:latest > $HOME/docker/image.tar
test:
override:
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