Mathias Goncalves

Alter FreeSurfer subjects to include session labels

1

### A short summary of what you would like to see in *NiBabies*. As we are moving to session-based processing, multiple runs of FreeSurfer can clash. We should probably alter...

Add regression test for `--cifti-output`

1

### A short summary of what you would like to see in *NiBabies*. As mentioned in #212 ### Do you have any interest in helping implement the feature? Yes! ###...

### A short summary of what you would like to see in *NiBabies*. - System / CPUs / Memory - Runtime duration - FreeSurfer run? - Precomputed outputs? ### Do...

### A short summary of what you would like to see in *NiBabies*. https://nibabies.readthedocs.io/en/latest/outputs.html is lacking ### Do you have any interest in helping implement the feature? Yes! ### Add...

### A short summary of what you would like to see in *NiBabies*. To allow anyone to run nibabies ### Do you have any interest in helping implement the feature?...

### A short summary of what you would like to see in *NiBabies*. In #212 we had to [backport](https://github.com/nipreps/nibabies/blob/22.0.2/nibabies/utils/viz.py) an earlier version of `fMRIPlot` to avoid drastically changing the workflow....

Verify default value for CIFTI subcortical volume smoothing

4

https://github.com/nipreps/nibabies/blob/8bcf2d7a7df8d8806722353000453cad2af7547b/nibabies/workflows/bold/alignment.py#L8 [Original implementation](https://github.com/DCAN-Labs/dcan-infant-pipeline/blob/bf2e295e49f586d8bce6e9e40ca1400b2a28d030/fMRISurface/scripts/SubcorticalAlign_ROIs.sh#L38) > ${SmoothingFWHM} / ( 2 * ( sqrt ( 2 * l ( 2 ) ) ) )

Change default output space to `MNI152NLin2009cAsym`

3

### A short summary of what you would like to see in *NiBabies*. To convene with fMRIPrep's outputs ### Do you have any interest in helping implement the feature? Yes!...

Ensure laplacians are used for registration

1

They are being fed into antsRegistration https://github.com/nipreps/nibabies/blob/c607811c719cc8e9fed03f9b748cd17818452ddb/nibabies/workflows/anatomical/brain_extraction.py#L274 and show up in the `report.rst` ``` * fixed_image : ['/work/nibabies_wf/single_subject_01_wf/infant_anat_wf/infant_brain_extraction_wf/clip_t2w_inu/clipped.nii.gz', '/work/nibabies_wf/single_subject_01_wf/infant_anat_wf/infant_brain_extraction_wf/norm_lap_t2w/clipped.nii.gz'] ... * moving_image : ['/work/nibabies_wf/single_subject_01_wf/infant_anat_wf/infant_brain_extraction_wf/clip_t1w_inu/clipped.nii.gz', '/work/nibabies_wf/single_subject_01_wf/infant_anat_wf/infant_brain_extraction_wf/norm_lap_t1w/clipped.nii.gz'] ``` But are nowhere to...

### A short summary of what you would like to see in *NiBabies*. Brains on the smaller size include excess background within reports. View should be zoomed in accordingly. ###...