niworkflows
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Common workflows for MRI (anatomical, functional, diffusion, etc)
Follow-up to #628, I think the `concat_images(four_to_three())` idiom is clear and concise, but not memory efficient in many cases. We may want to come up with another idiom to do...
If a dataset contains a compressed and uncompressed version of a file that will be operated on, the behavior or downstream tools may change. sMRIPrep will align and average a...
Coming out from https://github.com/nipreps/niworkflows/pull/610#discussion_r570260072 Although, I'm still not sure ``StructuralReference`` is a bad name. We are indeed calculating "structural" images (as in, with the maximal structural contrast as possible). If...
The idea is to avoid most of the massaging happening inside the old pipeline, since the references generated with the new workflow (#610) are ready for masking/registration. In particular, the...
Complementing #610, it would be beneficial to produce transforms that ``antsApplyTransform`` can digest. This is necessary for #613.
Seems like we have some inflexible configurations that made fMRIPrep/rodents fail with: ``` Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep-rodents", line 8, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep_rodents/cli/run.py", line 171, in main...
Ahoi hoi there, I have a question (maybe feature request) concerning the [reports package/module](https://www.nipreps.org/niworkflows/master/api/niworkflows.reports.core.html). For a while now, I'm trying to utilize it over at [BIDSonym](https://github.com/PeerHerholz/BIDSonym) to generate output reports...
https://github.com/nipreps/niworkflows/blob/3120884336dd9c3b6211eeb538ed5f2d1085ac78/niworkflows/cli/boldref.py#L51 specifically the generated mask: - `/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz` and likely the report: - `/mask_reportlet/report.svg`
This is not a bug, but an invitation to ourselves for thinking whether there is any possibility of getting a better result on these edge cases: ds005/sub-06: ![Screen Shot 2020-09-19...
### What version of fMRIPrep are you using? 20.2.0rc0 ### What kind of installation are you using? Containers (Singularity, Docker), or "bare-metal"? TACC Run ### Did fMRIPrep generate the visual...