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Initial sketch for the mriqc/fmriprep singularity based workflow #438

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Initial sketch for the mriqc/fmriprep singularity based workflow #438

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8f4469e
Initial sketch for the mriqc/fmriprep singularity based workflow
yarikoptic Jul 18, 2019
de0442f
DOC: added a few comments
yarikoptic Jul 18, 2019
a18521d
DOC: note on execution of mriqc
yarikoptic Jul 18, 2019
92388ed
ENH: make possible to quickly switch from reproman to datalad + some …
yarikoptic Aug 6, 2019
1588f76
ENH: text2git for mriqc output
yarikoptic Aug 6, 2019
5b95ded
BF: make get_participants_ids work + set -x for debugging
yarikoptic Aug 15, 2019
79c3a99
another perspective one on kwyk
yarikoptic Aug 21, 2019
57b6b6c
ENH/RF: shellcheck, group common bids-app logic into run_bids_app, ex…
yarikoptic Oct 10, 2019
fedb8b0
moved datalad install containers before working in containers subdir
chaselgrove Dec 12, 2019
dc5dc0b
Merge branch 'master' into doc-usecases
chaselgrove Dec 17, 2019
76450af
RF: compose proper call for fmriprep, inline querying participant labels
yarikoptic Dec 19, 2019
850b36f
RF: reordered commands so settings come first and then all the actions
yarikoptic Dec 19, 2019
7110ec6
BF+RF: improve handling of fs license, more TODO comments (seems to w…
yarikoptic Dec 19, 2019
a81e457
ENH: do not create bids app results dataset if directory exists already
yarikoptic Dec 20, 2019
d5e9028
defaulting RM_RESOURCE and RM_SUB to local but allowing overrides
chaselgrove Jan 3, 2020
924980c
Merge remote-tracking branch 'origin/master' into doc-usecases
yarikoptic Jan 8, 2020
d05430d
Merge branch 'doc-usecases' of https://github.com/yarikoptic/ReproNim…
yarikoptic Jan 8, 2020
5ab5a8b
clean the containers repo after freezing versions
chaselgrove Jan 14, 2020
7ae46ab
Revert "clean the containers repo after freezing versions"
chaselgrove Jan 28, 2020
a4af6ba
Merge branch 'master' into doc-usecases
chaselgrove Apr 27, 2020
5a2f0f3
Fix runscript regexp to work on Mac OS
chaselgrove Apr 29, 2020
b70144e
ENH: always set -x, add env vars to not require patching for FS licen…
yarikoptic May 21, 2020
82df248
Comments on which images must be prepropulated in containers repo and…
yarikoptic May 22, 2020
6009dd0
ENH: Script for reproducible rerun of the demo script
yarikoptic May 22, 2020
295d9d2
kyle1-ps4 setup
yarikoptic May 25, 2020
fc91ec2
Merge remote-tracking branch 'origin/master' into doc-usecases
yarikoptic May 25, 2020
8905cc4
BF: Fix failure on unset BIDS_APP with set -u
chaselgrove May 26, 2020
cffa3a3
BF: Add mac workaround in get_participant_ids
chaselgrove May 27, 2020
85a41dc
ENH: Update parallel install message for mac users
chaselgrove May 27, 2020
baab991
BF: export PS1 within -reproduce.sh
yarikoptic May 27, 2020
75fa815
ENH: Use temporary HOME, cp .gitconfig and .freesurfer-license, confi…
yarikoptic May 27, 2020
7920234
reproman-master setup for -reproduce and min datalad 0.12.7
yarikoptic May 27, 2020
29500a7
master reproman now has [datalad] installation target
yarikoptic May 28, 2020
3bf4e38
Merge remote-tracking branch 'origin/master' (needs datalad 0.13.0rc1…
yarikoptic May 28, 2020
d895cc4
ENH: add containers/licenses into --input, specify data/bids explicit…
yarikoptic May 28, 2020
e28d011
DOC: note that datalad runner group analysis probably does nothing
yarikoptic May 28, 2020
795eed8
ENH: point to subject specific input data
yarikoptic May 28, 2020
52c19fc
Merge remote-tracking branch 'yarik/doc-usecases' into doc-usecases
chaselgrove Jun 1, 2020
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1 change: 1 addition & 0 deletions docs/usecases/bids-fmriprep-workflow-NP.sh
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Expand Up @@ -222,6 +222,7 @@ containers/scripts/freeze_versions --save-dataset=^ \
poldracklab-ds003-example=0.0.3 \
bids-mriqc=0.15.0 \
bids-fmriprep=1.4.1
( cd containers/ ; git clean -dfx ; )
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@yarikoptic yarikoptic Jan 14, 2020

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Note: this is a temporary workaround to remove .datalad/config-e created by above freeze_versions script. Proper solution sounds fix that script to stay compatible with osx.


#
# Install dataset to be analyzed (no data - analysis might run in the cloud or on HPC)
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