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Merge pull request #14 from BIDS-Apps/fs6bug
Fs6bug
2 parents 84607b1 + 9a4b425 commit 2efaa34

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‎Dockerfile‎

Lines changed: 40 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,46 @@
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FROM fliem/tracula_base:fs6
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FROM bids/base_fsl
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#### FreeSurfer
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RUN apt-get -y update && \
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wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
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--exclude='freesurfer/subjects/fsaverage_sym' \
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--exclude='freesurfer/subjects/fsaverage3' \
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--exclude='freesurfer/subjects/fsaverage4' \
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--exclude='freesurfer/subjects/fsaverage5' \
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--exclude='freesurfer/subjects/fsaverage6' \
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--exclude='freesurfer/subjects/cvs_avg35' \
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--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
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--exclude='freesurfer/subjects/bert' \
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--exclude='freesurfer/subjects/V1_average' \
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--exclude='freesurfer/average/mult-comp-cor' \
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--exclude='freesurfer/lib/cuda' \
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--exclude='freesurfer/lib/qt'
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# Set up the environment
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ENV OS=Linux
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ENV FS_OVERRIDE=0
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ENV FIX_VERTEX_AREA=
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ENV SUBJECTS_DIR=/opt/freesurfer/subjects
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ENV FSF_OUTPUT_FORMAT=nii.gz
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ENV MNI_DIR=/opt/freesurfer/mni
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ENV LOCAL_DIR=/opt/freesurfer/local
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ENV FREESURFER_HOME=/opt/freesurfer
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ENV FSFAST_HOME=/opt/freesurfer/fsfast
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ENV MINC_BIN_DIR=/opt/freesurfer/mni/bin
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ENV MINC_LIB_DIR=/opt/freesurfer/mni/lib
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ENV MNI_DATAPATH=/opt/freesurfer/mni/data
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ENV FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast
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ENV PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5
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ENV MNI_PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5
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ENV PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
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RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
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RUN sudo apt-get update && apt-get install -y python3
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RUN sudo apt-get update && apt-get install -y python3-pip
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RUN pip3 install pybids pandas ipython
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RUN pip3 install pandas
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RUN pip3 install pybids
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RUN apt-get install -y tree htop
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RUN apt-get install -y tcsh

‎circle.yml‎

Lines changed: 8 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@ general:
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artifacts:
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- "~/outputs1"
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- "~/outputs2"
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machine:
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services:
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- docker #don't use 1.10 - caching is broken
@@ -23,33 +24,28 @@ dependencies:
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- docker build -t bids/${CIRCLE_PROJECT_REPONAME,,} . :
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timeout: 21600
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- mkdir -p ~/docker; docker save "bids/${CIRCLE_PROJECT_REPONAME,,}" > ~/docker/image.tar
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- mkdir -p ${HOME}/outputs
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test:
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override:
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# print version
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} --version
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# participant level tests for single session dataset
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep:
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep && cat ${HOME}/outputs1/sub-01/scripts/trac-preproc.done :
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timeout: 21600
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# - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02 --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep :
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# timeout: 21600
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# group level test for single session dataset: group1
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_tracula_precomp:/outputs -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group1 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_tracula_precomp/00_group* ${HOME}/outputs1/ :
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_tracula_precomp:/outputs -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group1 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_tracula_precomp/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group1_motion_stats/group_motion.tsv :
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timeout: 21600
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# group level test for single session dataset: group2
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_tracula_precomp:/outputs -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_tracula_precomp/00_group* ${HOME}/outputs1/ :
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_tracula_precomp:/outputs -v ${HOME}/data/ds114_test1_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_tracula_precomp/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group2_tract_stats/fminor_stats.tsv :
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timeout: 21600
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# participant level tests for a longitudinal dataset
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep :
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# participant level tests for a longitudinal dataset
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep && cat ${HOME}/outputs2/sub-01_ses-test.long.sub-01/scripts/trac-preproc.done :
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timeout: 21600
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# - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs -v ${HOME}/data/ds114_test2_freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02 --license_key="~/test.key" --freesurfer_dir /freesurfer --stages prep :
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# timeout: 21600
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# group level test for a longitudinal dataset: group1
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_tracula_precomp:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group1 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_tracula_precomp/00_group* ${HOME}/outputs2/ :
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_tracula_precomp:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group1 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_tracula_precomp/00_group* ${HOME}/outputs2/ && cat ${HOME}/outputs2/00_group1_motion_stats/group_motion.tsv :
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timeout: 21600
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# group level test for a longitudinal dataset: group2
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_tracula_precomp:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_tracula_precomp/00_group* ${HOME}/outputs2/ :
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- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_tracula_precomp:/outputs -v ${HOME}/data/ds114_test2_freesurfer:/freesurfer bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key" --freesurfer_dir /freesurfer && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_tracula_precomp/00_group* ${HOME}/outputs2/ && cat ${HOME}/outputs2/00_group2_tract_stats/fminor_stats.tsv:
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timeout: 21600
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deployment:

‎tracula.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -32,13 +32,13 @@ def get_data(layout, subject_label, freesurfer_dir, session_label=""):
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# long
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if session_label:
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# regex magic to avoid https://github.com/INCF/pybids/issues/25
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subject_session_info = {"subject": subject_label, "session": "^" + session_label + "$"}
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subject_session_info = {"subject": subject_label, "session": session_label}
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# cross
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else:
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subject_session_info = {"subject": subject_label}
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41-
dwi_files = [f.filename for f in layout.get(type="dwi", modality="dwi", ext="nii.gz", **subject_session_info)]
40+
dwi_files = [f.filename for f in layout.get(type="dwi", modality="dwi", extensions=["nii", "nii.gz"],
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**subject_session_info)]
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bvecs_files = layout.get_bvecs(**subject_session_info)
4343
if not bvecs_files:
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# if bvecs only in root dir

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