From 23085ede4a6b4e28bf4d2b445444a187a09dcb12 Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 13:37:18 +0100 Subject: [PATCH 01/10] now checks if .done file exists after prep test --- circle.yml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/circle.yml b/circle.yml index 077645d..60e1aab 100644 --- 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 @@ -30,21 +31,17 @@ test: # 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/ : 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/ : 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* ${HOME}/outputs2/ : timeout: 21600 From c784ccdda4107977f1be0dddd081119c718fbace Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 15:30:57 +0100 Subject: [PATCH 02/10] pybids extensions adaption --- tracula.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tracula.py b/tracula.py index 0870438..85c4324 100644 --- a/tracula.py +++ b/tracula.py @@ -38,7 +38,7 @@ def get_data(layout, subject_label, freesurfer_dir, session_label=""): else: subject_session_info = {"subject": subject_label} - dwi_files = [f.filename for f in layout.get(type="dwi", modality="dwi", ext="nii.gz", **subject_session_info)] + dwi_files = [f.filename for f in layout.get(type="dwi", modality="dwi", extensions="nii.gz", **subject_session_info)] bvecs_files = layout.get_bvecs(**subject_session_info) if not bvecs_files: # if bvecs only in root dir From ecf4f8f8eec355758dfc54aaf4f71066493597e0 Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 15:31:36 +0100 Subject: [PATCH 03/10] removed pybids regex magic https://github.com/INCF/pybids/issues/25 --- tracula.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tracula.py b/tracula.py index 85c4324..9b75b27 100644 --- a/tracula.py +++ b/tracula.py @@ -32,13 +32,13 @@ def get_data(layout, subject_label, freesurfer_dir, session_label=""): # long if session_label: - # regex magic to avoid https://github.com/INCF/pybids/issues/25 - subject_session_info = {"subject": subject_label, "session": "^" + session_label + "$"} + 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", extensions="nii.gz", **subject_session_info)] + dwi_files = [f.filename for f in + layout.get(type="dwi", modality="dwi", extensions="nii.gz", **subject_session_info)] bvecs_files = layout.get_bvecs(**subject_session_info) if not bvecs_files: # if bvecs only in root dir From a14ad8a06ad381f30611a1a5fc12354469136672 Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 15:54:27 +0100 Subject: [PATCH 04/10] cleanup --- circle.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/circle.yml b/circle.yml index 60e1aab..d72af32 100644 --- a/circle.yml +++ b/circle.yml @@ -24,7 +24,6 @@ dependencies: - docker build -t bids/${CIRCLE_PROJECT_REPONAME,,} . : timeout: 21600 - mkdir -p ~/docker; docker save "bids/${CIRCLE_PROJECT_REPONAME,,}" > ~/docker/image.tar - - mkdir -p ${HOME}/outputs test: override: From e195674e6c4e658072167d681d3c64ffd26a04ad Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 15:56:50 +0100 Subject: [PATCH 05/10] try docker without base image --- Dockerfile | 39 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ef05a37..8dde04e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,41 @@ -FROM fliem/tracula_base:fs6 +FROM bids/base_fsl + + +#### FreeSurfer +RUN apt-get -y update && \ + wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \ + --exclude='freesurfer/subjects/fsaverage_sym' \ + --exclude='freesurfer/subjects/fsaverage3' \ + --exclude='freesurfer/subjects/fsaverage4' \ + --exclude='freesurfer/subjects/fsaverage5' \ + --exclude='freesurfer/subjects/fsaverage6' \ + --exclude='freesurfer/subjects/cvs_avg35' \ + --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \ + --exclude='freesurfer/subjects/bert' \ + --exclude='freesurfer/subjects/V1_average' \ + --exclude='freesurfer/average/mult-comp-cor' \ + --exclude='freesurfer/lib/cuda' \ + --exclude='freesurfer/lib/qt' + +# Set up the environment +ENV OS=Linux +ENV FS_OVERRIDE=0 +ENV FIX_VERTEX_AREA= +ENV SUBJECTS_DIR=/opt/freesurfer/subjects +ENV FSF_OUTPUT_FORMAT=nii.gz +ENV MNI_DIR=/opt/freesurfer/mni +ENV LOCAL_DIR=/opt/freesurfer/local +ENV FREESURFER_HOME=/opt/freesurfer +ENV FSFAST_HOME=/opt/freesurfer/fsfast +ENV MINC_BIN_DIR=/opt/freesurfer/mni/bin +ENV MINC_LIB_DIR=/opt/freesurfer/mni/lib +ENV MNI_DATAPATH=/opt/freesurfer/mni/data +ENV FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast +ENV PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 +ENV MNI_PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 +ENV PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$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 From 44bf7e3509de81847478710da8388389755fd465 Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 16:04:10 +0100 Subject: [PATCH 06/10] check for restuls files in group* tests --- circle.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/circle.yml b/circle.yml index d72af32..2a961c5 100644 --- a/circle.yml +++ b/circle.yml @@ -33,19 +33,19 @@ test: - 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 # 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 && cat ${HOME}/outputs2/sub-01_ses-test.long.sub-01/scripts/trac-preproc.done : 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: From 5354724c47a68b23310d81851c01c29de9959e2a Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 17:18:45 +0100 Subject: [PATCH 07/10] pandas and pybids installation in sep lines to find new install issue. removed ipython --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ef05a37..77b2e6b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,8 @@ FROM fliem/tracula_base:fs6 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 From cabd244e7382e1aba95ac2f917a71a5349a96eab Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 18:06:28 +0100 Subject: [PATCH 08/10] typo --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index 2a961c5..6503d34 100644 --- a/circle.yml +++ b/circle.yml @@ -33,7 +33,7 @@ test: - 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 # 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/ && $cat {HOME}/outputs1/00_group1_motion_stats/group_motion.tsv : + - 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/ && cat ${HOME}/outputs1/00_group2_tract_stats/fminor_stats.tsv : From 2b0cdb68359b5db2fd273ee262fa9b59523e1e98 Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 18:48:23 +0100 Subject: [PATCH 09/10] typo again --- circle.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/circle.yml b/circle.yml index 6503d34..bb1757c 100644 --- a/circle.yml +++ b/circle.yml @@ -33,7 +33,7 @@ test: - 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 # 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/ && $cat ${HOME}/outputs1/00_group1_motion_stats/group_motion.tsv : + - 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/ && cat ${HOME}/outputs1/00_group2_tract_stats/fminor_stats.tsv : From 9a4b425748c6cd282b3d7d9e263969bda60304af Mon Sep 17 00:00:00 2001 From: fliem Date: Wed, 25 Jan 2017 22:36:11 +0100 Subject: [PATCH 10/10] added nii ext --- tracula.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tracula.py b/tracula.py index 9b75b27..804db42 100644 --- a/tracula.py +++ b/tracula.py @@ -37,8 +37,8 @@ def get_data(layout, subject_label, freesurfer_dir, session_label=""): else: subject_session_info = {"subject": subject_label} - dwi_files = [f.filename for f in - layout.get(type="dwi", modality="dwi", extensions="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