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Support independent jobs across sessions #1175
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I think one of the relevant problems to consider here is separate working directories, which will attempt to re-run anatomical. I think we need to ensure that all necessary anatomical inputs to the BOLD workflow are in the anatomical derivatives, and use those, rather than reaching into the working directory. I think at one point I had an open issue about a DataGrabber for fmriprep derivatives. That could be a useful component here. |
This is the key point here. +1 |
just wanted to upvote this one again (just trying to analyze myconnectome data again). |
Also bumping this much needed feature, so +1. |
This will be possible when nipreps/smriprep#107 is merged in. Can't provide an ETA, but I'd like to see this fixed within 2 months. |
Postponing this relabeling created a deviation of the derivative written out to the hard disk and the actual file passed on by the outputnode. This PR should serve as a basis for the elimination of FSL FAST in ``recon-all`` -based workflows (cc/ @mgxd): - FAST and the new tailgating node should be moved inside the if branch for ``--fs-no-reconall`` - The LUT mapping function should be reused to remap FS's ``aseg`` into a 3-tissue brain segmentation. Resolves: nipreps#176 Related: nipreps#170 Related: nipreps/fmriprep#1175
Postponing this relabeling created a deviation of the derivative written out to the hard disk and the actual file passed on by the outputnode. This PR should serve as a basis for the elimination of FSL FAST in ``recon-all`` -based workflows (cc/ @mgxd): - FAST and the new tailgating node should be moved inside the if branch for ``--fs-no-reconall`` - The LUT mapping function should be reused to remap FS's ``aseg`` into a 3-tissue brain segmentation. Resolves: nipreps#176 Related: nipreps#170 Related: nipreps/fmriprep#1175
Postponing this relabeling created a deviation of the derivative written out to the hard disk and the actual file passed on by the outputnode. This PR should serve as a basis for the elimination of FSL FAST in ``recon-all`` -based workflows (cc/ @mgxd): - FAST and the new tailgating node should be moved inside the if branch for ``--fs-no-reconall`` - The LUT mapping function should be reused to remap FS's ``aseg`` into a 3-tissue brain segmentation. Resolves: nipreps#176 Related: nipreps#170 Related: nipreps/fmriprep#1175
Postponing this relabeling created a deviation of the derivative written out to the hard disk and the actual file passed on by the outputnode. This PR should serve as a basis for the elimination of FSL FAST in ``recon-all`` -based workflows (cc/ @mgxd): - FAST and the new tailgating node should be moved inside the if branch for ``--fs-no-reconall`` - The LUT mapping function should be reused to remap FS's ``aseg`` into a 3-tissue brain segmentation. Resolves: nipreps#176 Related: nipreps#170 Related: nipreps/fmriprep#1175
Postponing this relabeling created a deviation of the derivative written out to the hard disk and the actual file passed on by the outputnode. This PR should serve as a basis for the elimination of FSL FAST in ``recon-all`` -based workflows (cc/ @mgxd): - FAST and the new tailgating node should be moved inside the if branch for ``--fs-no-reconall`` - The LUT mapping function should be reused to remap FS's ``aseg`` into a 3-tissue brain segmentation. Resolves: nipreps#176 Related: nipreps#170 Related: nipreps/fmriprep#1175
… given Summary ------- This PR utilizes nipreps/smriprep#107 to allow a fast skip of the anatomical workflow evaluation, and the need of maintaining the work directory for it. Closes nipreps#1175 Changes suggested ----------------- * [x] Added an ``--anat-derivatives`` flag to the command line. * [x] Integrated the new flag with the new config module. * [x] Estimate existing derivatives using *sMRIPrep*'s tooling. * [x] Pass in the existing derivatives and nipreps/smriprep#107 skips the anatomical workflow fulfilling the workflow API. Potential problems ------------------ This PR does not contain any measures to preserve the reproducibility of *fMRIPrep* if the fast-track is used.
It's certain that we will see more and more datasets like MyConnectome and Midnight Scan Club. To efficiently process such dataset we need to support submitting independent jobs across sessions. In practice this would mean:
session
analysis level and--session_label
flag for selecting sessions (more details at https://groups.google.com/forum/#!topic/bids-apps-dev/Vnx5HHudqq4)participant_anat
analysis level to be run before anysession
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