Superficial White Matter
This module samples superficial white matter intensities from a quantitative MRI in nativepro space. This is achieved by constructing a series of equivolumetric surfaces between the gray matter boundary and 3 mm below it following a laplacian field.
Superficial white matter surfaces are generated using scripts from the superficial-white-matter repository, available via GitHub by Jordan De Kraker.
-SWM
Prerequisites 🖐🏼
You need to run -proc_structural
, -proc_surf
and -post_structural
before this stage
Generate 3 equivolumetric SWM surfaces between the gray matter boundary and 3 mm below it.
Map qMRI SWM surfaces to fsLR-32k, fsLR-5k and fsaverage5.
Terminal:
$ micapipe -sub <subject_id> -out <outputDirectory> -bids <BIDS-directory> -SWM
Optional arguments:
-SWM
does not optional arguments:
Directories created or populated by -SWM:
- <outputDirectory>/micapipe_v0.2.0/<sub>/surf
- <outputDirectory>/micapipe_v0.2.0/<sub>/maps
Files generated by -SWM:
- Surfaces: <outputDirectory>/micapipe_v0.2.0/<sub>/surf/ <sub>_<ses>_<hemi>_space_fsnative_label_swm1.0mm.surf.gii <sub>_<ses>_<hemi>_space_fsnative_label_swm2.0mm.surf.gii <sub>_<ses>_<hemi>_space_fsnative_label_swm3.0mm.surf.gii - Maps: <outputDirectory>/micapipe_v0.2.0/<sub>/maps/ <sub>_<ses>_<hemi>_surf_fsnative_label_1.0mm_<qMRI>.func.gii <sub>_<ses>_<hemi>_surf_fsnative_label_2.0mm_<qMRI>.func.gii <sub>_<ses>_<hemi>_surf_fsnative_label_3.0mm_<qMRI>.func.gii