Merge pull request #14 from BIDS-Apps/fs6bug

Fs6bug
bids-apps · Jan 26, 2017 · 2efaa34 · 2efaa34
2 parents 84607b1 + 9a4b425
commit 2efaa34
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diff --git a/Dockerfile b/Dockerfile
@@ -1,8 +1,46 @@
-FROM fliem/tracula_base:fs6
+FROM bids/base_fsl
+
+
+#### FreeSurfer
+RUN apt-get -y update && \
+    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 \
+    --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'
+
+# Set up the environment
+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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
+RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
+
 
 RUN sudo apt-get update && apt-get install -y python3
 RUN sudo apt-get update && apt-get install -y python3-pip
-RUN pip3 install pybids pandas ipython
+RUN pip3 install pandas
+RUN pip3 install pybids
 
 RUN apt-get install -y tree htop
 RUN apt-get install -y tcsh

diff --git a/circle.yml b/circle.yml
@@ -2,6 +2,7 @@ general:
   artifacts:
     - "~/outputs1"
     - "~/outputs2"
+
 machine:
   services:
     - docker #don't use 1.10 - caching is broken
@@ -23,33 +24,28 @@ dependencies:
     - docker build -t bids/${CIRCLE_PROJECT_REPONAME,,} . :
         timeout: 21600
     - mkdir -p ~/docker; docker save "bids/${CIRCLE_PROJECT_REPONAME,,}" > ~/docker/image.tar
-    - mkdir -p ${HOME}/outputs
 
 test:
   override:
     # print version
     - 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
     # participant level tests for single session dataset
-    - 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:
+    - 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 :
         timeout: 21600
-    # - 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 :
-    #     timeout: 21600
     # group level test for single session dataset: group1
-    - 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/ :
+    - 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 :
         timeout: 21600
     # group level test for single session dataset: group2
-    - 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/ :
+    - 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 :
         timeout: 21600
-  # participant level tests for a longitudinal dataset
-    - 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 :
+    # participant level tests for a longitudinal dataset
+    - 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 :
         timeout: 21600
-    # - 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 :
-    #     timeout: 21600
     # group level test for a longitudinal dataset: group1
-    - 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/ :
+    - 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 :
         timeout: 21600
     # group level test for a longitudinal dataset: group2
-    - 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/ :
+    - 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:
         timeout: 21600
 
 deployment:

diff --git a/tracula.py b/tracula.py
@@ -32,13 +32,13 @@ def get_data(layout, subject_label, freesurfer_dir, session_label=""):
 
     # long
     if session_label:
-        # regex magic to avoid https://github.com/INCF/pybids/issues/25
-        subject_session_info = {"subject": subject_label, "session": "^" + session_label + "$"}
+        subject_session_info = {"subject": subject_label, "session": session_label}
     # cross
     else:
         subject_session_info = {"subject": subject_label}
 
-    dwi_files = [f.filename for f in layout.get(type="dwi", modality="dwi", ext="nii.gz", **subject_session_info)]
+    dwi_files = [f.filename for f in layout.get(type="dwi", modality="dwi", extensions=["nii", "nii.gz"],
+                                                **subject_session_info)]
     bvecs_files = layout.get_bvecs(**subject_session_info)
     if not bvecs_files:
         # if bvecs only in root dir