use single pybids_inputs instead of two

[akhanf]

Removes pybids_inputs_dwi.

Having two was problematic since the pybids_inputs_dwi wasn't changeable from the CLI options.

Proposed changes

Find/replace:
pybids_inputs_dwi -> pybids_inputs
inputs_t1 -> inpts
inputs_dwi -> inputs
mask -> dwi_mask

So far only dry-run testing done, but that should be sufficient given the change.

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[Dhananjhay]

Looks good! I was also able to get the dry test run working but I had to change the aparcaseg input parameter in the mgz2nii rule to point to the right location. However, I can't seem to test the wet run because it says permission denied when I try to write at the freesurfer's location.

[akhanf]

interesting -- what data are you running it on? It would be good to have a small (single-subject) wet-run dataset to dig into that, perhaps could post an open access one to GIN?

[Dhananjhay]

Hmm I was just using the dummy test data that is shipped along with scattr. I run the following command for the dry run:

scattr scattr/test/data/bids derivatives participant --cores all -np --fs-license /srv/software/freesurfer/7.4.1/license.txt --freesurfer_dir /srv/software/freesurfer/7.4.1/

where I had to change

aparcaseg=str(
      Path(bids(root=freesurfer_dir, **inputs.subj_wildcards)).parent
      / "mri"
      / "aparc+aseg.mgz"
),

to

aparcaseg='/srv/software/freesurfer/7.4.1/subjects/fsaverage/mri/aparc+aseg.mgz'

For the wet run I couldn't find any suitable data from openneuro so I just tried the above command without the np flag just for experiment purposes but I guess it tries to write files at --freesurfer_dir /srv/software/freesurfer/7.4.1/ and therefore runs into permission issues. I agree re: (single-subject) wet-run and maybe we can extrapolate this into a Continuous integration (CI) test setup on github for scattr since it's pretty lightweight. What do you think?

[akhanf]

Ah I see, actually the --freesurfer_dir cli arg is meant for pointing to where the freesurfer subjects dir is, ie where freesurfer has been run on the subject(s), not the freesurfer software dependency (that's in the container).

It also write files to the freesurfer folder when it runs the additional freesurfer thalamic subnuclei segmentation (since it runs atop freesurfer recon-all).

But for the wet run you would need to have freesurfer already run, as well as the diffusion data preprocessed, and the T1w brain-masked.

[Dhananjhay]

I just ran a limited wet run test to test this out and I think this PR is good to merge!

Test command:
scattr /project/ctb-akhanf/djay/synthstrip test-scattr participant --participant-label P003 --freesurfer_dir /project/ctb-akhanf/djay/fmriprep_all/sourcedata/freesurfer --path_dwi /project/ctb-akhanf/mliu366/4_SNSX_7T/derivatives/prepdwi_v0.0.13/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_dwi.nii.gz --path-mask /project/ctb-akhanf/mliu366/4_SNSX_7T/derivatives/prepdwi_v0.0.13/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_mask.nii.gz --cores all --fs-license ${FS_LICENSE_FILE} --show-failed-logs --use-singularity --bzero_thresh 50 --rerun-incomplete --filter-T1w desc=synthstrip --until tckgen --omit-from tckgen