Taylor Salo

Fix FUGUE bug

3

Closes #752. ## Changes proposed in this pull request - Add test using multi-shell DWI data with a GRE field map, using data from https://openneuro.org/datasets/ds005299/versions/1.0.0. - Add single-shell + GRE...

These methods use regular expressions to find sidecar JSON files. Now that QSIPrep has access to the BIDSLayout through the config object, there's no need to rely on custom code...

### What went wrong? I am trying to clone my dataset ([ds005250](https://openneuro.org/datasets/ds005250)) with datalad. When trying to `datalad get` certain files, I get the following error: ``` get(error): sub-02/ses-1/func/sub-02_ses-1_task-rest_acq-MBME_run-02_echo-5_part-mag_bold.nii.gz (file)...

ENH: Support combined surface-volume reference spaces

1

Closes #881. This is a ways away from being usable, but it might be good to get folks' thoughts on it before I put too much effort into it. Changes...

### What happened? The reference space dimension check in `niworkflows.utils.spaces.Reference` only looks at the name of the space to determine if it's 2D (i.e., a surface): https://github.com/nipreps/niworkflows/blob/1dc0327aa10f156fde480ec0b23c61a026b8022a/niworkflows/utils/spaces.py#L168-L169 However, there are...

Distinguish between surface and volume spaces in `Reference`

3

### What would you like to see added in this software? In order to parse surface-volume combinations for CIFTIs, I think `Reference` needs to be able to distinguish between the...

It looks like the sphere files needed to warp from fsLR to fsaverage are on TemplateFlow: ``` tpl-fsLR_space-fsaverage_hemi-L_den-164k_sphere.surf.gii tpl-fsLR_space-fsaverage_hemi-L_den-32k_sphere.surf.gii tpl-fsLR_space-fsaverage_hemi-L_den-59k_sphere.surf.gii tpl-fsLR_space-fsaverage_hemi-R_den-164k_sphere.surf.gii tpl-fsLR_space-fsaverage_hemi-R_den-32k_sphere.surf.gii tpl-fsLR_space-fsaverage_hemi-R_den-59k_sphere.surf.gii ``` Could we add the corresponding one...

Add `space-fsaverage` to `desc-reg` sphere files without space entity

2

### A short summary of what you would like to see in *NiBabies*. I've seen outputs from Nibabies with the following naming convention: `_hemi-_desc-reg_sphere.surf.gii`. Based on [a discussion](https://mattermost.brainhack.org/brainhack/pl/deqrcp7pxf8bpcu14cq97tc4rr) with @effigies,...

### A short summary of what you would like to see in *NiBabies*. My understanding is that the resulting surface files will have the same vertices and mesh as the...