T1b — Registration & Parcellation
- T1b brings subject brain into standard space (MNI, FSAVG, parcellation maps exist in standard space)
- You have different kinds of transforms
- 6dof — linear transformation
- 12dof — nonlinear transformation
- FNIRT — warping
- By bringing subjects to MNI space, you generate instructions that you can use to bring parcellation maps to native space
- Parcellation Maps
- Different kinds of “standard” brains
- e.g. Schaefer 2000, Schaefer subcortical
- Schaefer Atlas (or yeo atlas, etc.)
- Subdivides regions into functional networks
- e.g. all ‘1’s are the visual network
- To stay in MNI space or to go to subject?
- The norm is to stay in MNI space, but for some analyses you want to bring the parcellation maps down into standard space
- e.g. if you don’t care about individual differences in each map, stay in MNI
- data isn’t always good enough to bring it down into native space
- Segmentation
- Chop, mask, etc to ensure that the parcellation maps are only on the grey matter
- Make masks of CSF, White matter, and grey matter. Use these to find ideal grey matter masks (binary, is it or is it not)
- Combine masks of unnecessary stuff (white matter, csf, etc) and use it to eliminate them from the grey matter mask
- Erosion: erode the masks to make them just lines
- Get subcortical structures
- fsl_anat allows for most of T1a and T1b, we just use it to grab the subcortical structures
References