T1 and T2 preproc anatomical derivatives are skull stripped for mcribs and infantfs reconstruction methods

[lundq163]

What happened?

Particularly when using mcribs and infantfs for surface reconstruction, the preproc T1w and T2w anatomical derivatives are skull stripped. While when using adult freesurfer for surface reconstruction these same derivatives are not skull stripped. It is my understanding that none of the derivatives should be skull stripped regardless of surface reconstruction method.

Below is an example run command and the directory structure of the external derivatives that were passed in:

What command did you use?

singularity run --cleanenv \
	-B /tmp/bids_dir/sub-100619_ses-17mo:/bids_dir \
	-B /tmp/processed/nibabies/sub-100619_ses-17mo:/output_dir \
	-B /tmp/work_dir/nibabies/sub-100619_ses-17mo:/wd \
	-B /tmp/processed/bibsnet/sub-100619_ses-17mo:/derivatives \
	-B /tmp/license.txt:/license.txt \
	 /home/faird/shared/code/external/pipelines/nibabies/nibabies_24.0.0.sif \
	 /bids_dir /output_dir participant \
	--output-spaces MNI152NLin6Asym:res-2 \
	--fs-license-file /license.txt \
	--omp-nthreads 8 \
	--nprocs 8 \
	--cifti-output 91k \
	-vv \
	--project-goodvoxels \
	--fd-radius 45 \
	--derivatives /derivatives \
	--surface-recon-method infantfs \
	--age-months 17mo \
	-w /wd


sub-100619/
    ses-17mo/
        anat/
             sub-100619_ses-17mo_space-T1w_desc-aseg_dseg.json
             sub-100619_ses-17mo_space-T1w_desc-aseg_dseg.nii.gz
             sub-100619_ses-17mo_space-T1w_desc-aseg_volumes.json
             sub-100619_ses-17mo_space-T1w_desc-aseg_volumes.tsv
             sub-100619_ses-17mo_space-T1w_desc-brain_mask.json
             sub-100619_ses-17mo_space-T1w_desc-brain_mask.nii.gz
             sub-100619_ses-17mo_space-T2w_desc-aseg_dseg.json
             sub-100619_ses-17mo_space-T2w_desc-aseg_dseg.nii.gz
             sub-100619_ses-17mo_space-T2w_desc-aseg_volumes.json
             sub-100619_ses-17mo_space-T2w_desc-aseg_volumes.tsv
             sub-100619_ses-17mo_space-T2w_desc-brain_mask.json
             sub-100619_ses-17mo_space-T2w_desc-brain_mask.nii.gz

2 directories, 12 files

What version of NiBabies are you using?

24.0.0

Relevant log output

No response

Add any additional information or context about the problem here.

Please let me know if anything else is needed, thank you!

[mgxd]

Fixed in #400