Expected structural outputs

[mgxd]

Below is a list of sMRIPrep outputs. All T1w files will likely be replace with T2w, since that's what nirodents primarily uses. @eilidhmacnicol does this list look right?

• [x] t1w_preproc The T1w reference map, which is calculated as the average of bias-corrected and preprocessed T1w images, defining the anatomical space.

• [x] t1w_brain Skull-stripped t1w_preproc

• [x] t1w_mask Brain (binary) mask estimated by brain extraction.

• [x] t1w_dseg Brain tissue segmentation of the preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF).

• [x] t1w_tpms List of tissue probability maps corresponding to t1w_dseg.

• [x] std_preproc T1w reference resampled in one or more standard spaces.

• [x] std_mask Mask of skull-stripped template, in MNI space

• [x] std_dseg Segmentation, resampled into MNI space

• [x] std_tpms List of tissue probability maps in MNI space

• [ ] subjects_dir FreeSurfer SUBJECTS_DIR

• [x] anat2std_xfm Nonlinear spatial transform to resample imaging data given in anatomical space into standard space.

• [x] std2anat_xfm Inverse transform of the above.

• [ ] subject_id FreeSurfer subject ID

• [ ] t1w2fsnative_xfm LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space

• [ ] fsnative2t1w_xfm LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w

• [ ] surfaces GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)

[eilidhmacnicol]

LGTM.

Although the std_* outputs won't be in "MNI space", but whatever standard space is associated with the template (probably WHS, for instance).