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Issue #29 #30

Merged
merged 16 commits into from
Aug 3, 2017
Merged

Issue #29 #30

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6b48d51
Allowing to execute longitudinal steps separately
ntraut Mar 14, 2017
61ddc62
Allowing to execute longitudinal steps separately
ntraut Mar 14, 2017
15bb340
skipping already segmented subjects
ntraut Mar 14, 2017
6f2460d
skip sessions without T1w images
ntraut Mar 14, 2017
655fa8e
allowing to run sessions separately
ntraut Mar 16, 2017
325d035
fix of resume command for template creation in longitudinal pipeline
ntraut Mar 20, 2017
0a1b4e4
bug fix with session_label option
ntraut Mar 21, 2017
1b22302
use python2 for freesurfer scripts
ntraut May 16, 2017
7d14165
skip subject if he does not have a T1 image in single session studies
ntraut May 16, 2017
5f4fe37
merge with upstream
ntraut May 16, 2017
8393a9d
fixing python 2 ubuntu package name
ntraut May 16, 2017
0eb2cc3
merge with upstream
ntraut May 18, 2017
d8e71da
merge with upstream
ntraut May 18, 2017
432c726
renaming longitudinal pipeline steps names
ntraut Jun 1, 2017
88f1038
adding a test for longitudinal pipeline decomposition
ntraut Jun 1, 2017
bf10e11
adding a test for longitudinal pipeline decomposition
ntraut Jun 1, 2017
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2 changes: 2 additions & 0 deletions circle.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,8 @@ test:
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset bids/${CIRCLE_PROJECT_REPONAME,,} --version
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --stages autorecon1 && cat ${HOME}/outputs1/sub-01/scripts/recon-all.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 ${HOME}/outputs2:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --steps cross-sectional --session_label test --license_key="~/test.key" --stages autorecon1 && cat ${HOME}/outputs2/sub-01_ses-test/scripts/recon-all.done :
timeout: 21600
# group2 tests
- docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key" && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv :
timeout: 21600
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