Rename "T1w" space to "anat"

[tsalo]

This stems from #2233 (comment), in which @effigies proposed that the T1w space should be renamed to "individual", to match BIDS terminology for participant-specific anatomical space (see here).

[effigies]

Thanks, Taylor. @oesteban, do you agree?

[oesteban]

I'm not particularly against it, but names will be considerably longer - which is not great.

[tsalo]

Would this apply to workflow names and variables as well? E.g., fmriprep.registration.init_bold_t1_trans_wf() --> fmriprep.registration.init_bold_individual_trans_wf().

EDIT: I assume we wouldn't use the scanner term in the code, since scanner can refer to native space for any datatype.

[effigies]

I think it would just be derivatives.

I'm okay with not doing this, if space-T1w is still BIDS conformant.

[oesteban]

BTW, if we push for individual, we'll need to update the config (see nipreps/niworkflows#540)

[tsalo]

I'd like to revisit this given that, in Nibabies, the primary anatomical modality may be T1w or T2w, so a general space label would be helpful for post-processing pipelines like XCP-D. This came up recently for QSIPrep/QSIRecon as well: PennLINC/qsiprep#853.

I'm not sure anyone wants to use "individual" specifically, but what about something like space-anat?

[effigies]

I think anat is reasonable. We're increasingly using it internally to be T1w/T2w-agnostic.

[tsalo]

That sounds great. It seems like this could end up being distinct from T1w or T2w (at least for the secondary anatomical contrast). For example, with fMRIPrep, where T1w is the primary anatomical contrast, we could end up with the following:

sub-X_desc-preproc_T1w.nii.gz  # native T1w space
sub-X_desc-preproc_T2w.nii.gz  # native T2w space, different from T1w space
sub-X_space-anat_desc-preproc_T1w.nii.gz  # same as sub-X_desc-preproc_T1w.nii.gz
sub-X_space-anat_desc-preproc_T2w.nii.gz  # in native T1w space

For Nibabies, where T2w is the primary anatomical contrast, space-anat and T2w without a space entity would be the same instead:

sub-X_desc-preproc_T1w.nii.gz  # native T1w space
sub-X_desc-preproc_T2w.nii.gz  # native T2w space, different from T1w space
sub-X_space-anat_desc-preproc_T1w.nii.gz  # in native T2w space
sub-X_space-anat_desc-preproc_T2w.nii.gz  # same as sub-X_desc-preproc_T2w.nii.gz

[effigies]

I'd probably rather apply it everywhere than imply which image defines the space in other images by omitting it for the defining image.

[effigies]

Ah, just reread, and I agree with your post.