niworkflows
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nipreps
Common workflows for MRI (anatomical, functional, diffusion, etc)
Working on https://github.com/nipreps/fmriprep/issues/1550. Relies on an updated version of the gradunwarp https://github.com/bpinsard/gradunwarp/tree/fix/mem_leaks.
In fMRIPrep docs, we use: ```RST :class:`niworkflows.interfaces.freesurfer.RefineBrainMask` ``` The resulting link is: https://www.nipreps.org/niworkflows/api/niworkflows.interfaces.freesurfer.html#niworkflows.interfaces.freesurfer.RefineBrainMask It should be: https://www.nipreps.org/niworkflows/1.7/api/niworkflows.interfaces.freesurfer.html#niworkflows.interfaces.freesurfer.RefineBrainMask
### What happened? https://github.com/nipreps/niworkflows/pull/739 added a check that a certain file exists in a pre-existing FreeSurfer directory. If the directory is being copied by another simultaneous job, then portions of...
### What happened? If pandoc fails to fully convert the Markdown boilerplate, our report compilation can fail here: https://github.com/nipreps/niworkflows/blob/065c2b6fcab73afc64441708c911a7ecfceba1f2/niworkflows/reports/core.py#L404-L408 We should code a bit more defensively and allow for regexes...
We are trying to re-run a dataset previously processed with fmriprep 20.2.0, now with 20.2.7, re-using the freesurfer runs from 20.2.0 . The 20.2.0 runs exist on a read-only folder....
### What happened? Replace current functionalities with shims that spit out deprecation warnings. ### What command did you use? ```shell n/a ``` ### What version of fMRIPrep are you running?...
Derivatives specification says if the `res` entitiy is used `Resolution` must be defined in its json file: https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#preprocessed-coregistered-andor-resampled-volumes The actual content of the `Resolution` field is pretty wide open so...
### What happened? While inspecting fmriprep 21.0.2 results I ran into this failed tissue segmentation, while it was succesful in 20.2.6. Any idea how I can fix this for the...
