-
Notifications
You must be signed in to change notification settings - Fork 14
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Initial sketch for the mriqc/fmriprep singularity based workflow #438
Draft
yarikoptic
wants to merge
38
commits into
ReproNim:master
Choose a base branch
from
yarikoptic:doc-usecases
base: master
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Draft
Changes from 1 commit
Commits
Show all changes
38 commits
Select commit
Hold shift + click to select a range
8f4469e
Initial sketch for the mriqc/fmriprep singularity based workflow
yarikoptic de0442f
DOC: added a few comments
yarikoptic a18521d
DOC: note on execution of mriqc
yarikoptic 92388ed
ENH: make possible to quickly switch from reproman to datalad + some …
yarikoptic 1588f76
ENH: text2git for mriqc output
yarikoptic 5b95ded
BF: make get_participants_ids work + set -x for debugging
yarikoptic 79c3a99
another perspective one on kwyk
yarikoptic 57b6b6c
ENH/RF: shellcheck, group common bids-app logic into run_bids_app, ex…
yarikoptic fedb8b0
moved datalad install containers before working in containers subdir
chaselgrove dc5dc0b
Merge branch 'master' into doc-usecases
chaselgrove 76450af
RF: compose proper call for fmriprep, inline querying participant labels
yarikoptic 850b36f
RF: reordered commands so settings come first and then all the actions
yarikoptic 7110ec6
BF+RF: improve handling of fs license, more TODO comments (seems to w…
yarikoptic a81e457
ENH: do not create bids app results dataset if directory exists already
yarikoptic d5e9028
defaulting RM_RESOURCE and RM_SUB to local but allowing overrides
chaselgrove 924980c
Merge remote-tracking branch 'origin/master' into doc-usecases
yarikoptic d05430d
Merge branch 'doc-usecases' of https://github.com/yarikoptic/ReproNim…
yarikoptic 5ab5a8b
clean the containers repo after freezing versions
chaselgrove 7ae46ab
Revert "clean the containers repo after freezing versions"
chaselgrove a4af6ba
Merge branch 'master' into doc-usecases
chaselgrove 5a2f0f3
Fix runscript regexp to work on Mac OS
chaselgrove b70144e
ENH: always set -x, add env vars to not require patching for FS licen…
yarikoptic 82df248
Comments on which images must be prepropulated in containers repo and…
yarikoptic 6009dd0
ENH: Script for reproducible rerun of the demo script
yarikoptic 295d9d2
kyle1-ps4 setup
yarikoptic fc91ec2
Merge remote-tracking branch 'origin/master' into doc-usecases
yarikoptic 8905cc4
BF: Fix failure on unset BIDS_APP with set -u
chaselgrove cffa3a3
BF: Add mac workaround in get_participant_ids
chaselgrove 85a41dc
ENH: Update parallel install message for mac users
chaselgrove baab991
BF: export PS1 within -reproduce.sh
yarikoptic 75fa815
ENH: Use temporary HOME, cp .gitconfig and .freesurfer-license, confi…
yarikoptic 7920234
reproman-master setup for -reproduce and min datalad 0.12.7
yarikoptic 29500a7
master reproman now has [datalad] installation target
yarikoptic 3bf4e38
Merge remote-tracking branch 'origin/master' (needs datalad 0.13.0rc1…
yarikoptic d895cc4
ENH: add containers/licenses into --input, specify data/bids explicit…
yarikoptic e28d011
DOC: note that datalad runner group analysis probably does nothing
yarikoptic 795eed8
ENH: point to subject specific input data
yarikoptic 52c19fc
Merge remote-tracking branch 'yarik/doc-usecases' into doc-usecases
chaselgrove File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
DOC: note on execution of mriqc
commit a18521d10ce085083a670372393bcd022cc5fbb6
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
so the original, datalad command would be
TODO : add inputs/outputs specification