This is an old revision of the document!
Surface-based Analysis (cifti)
Surface files track vertices instead of volumetric voxels. Files are created by tools like xcpd.
Types
citfi files have double extentions like *.dscalar.nii. See https://balsa.wustl.edu/about/fileTypes for more. From there, highlights are:
| dscalar | one or more dense maps of scalar values (e.g., myelin maps, curvature maps) |
|---|---|
| dtseries | one or more dense timeseries datasets (e.g., fMRI timeseries) or other data at equal intervals |
| dlabel | one or more dense maps of integer values, plus a ‘label table’ that defines each integer (e.g., one or more parcellations of cerebral cortex, subcortical nuclei, or all grayordinates) |
| pscalar | one or more parcellated scalar maps (e.g., a parcellated thickness map having uniform thickness within each parcel |
| ptseries | parcellated timeseries |
| plabel | one or more parcel maps, where each parcel is identified and colored using a label |
Working with surface data in R
See Val's tutorial on github https://github.com/PennLINC/surfaces_R_tutorial/blob/main/surface_tools_R.Rmd which covers information about cifti files and the fslr surface, types of ciftis/giftis, and how to read, manipulate, write, and visualize dense and parcellated cortical surface data in R
Working with surface data using Connectome Workbench
Connectome workbench has a ton of tools for working with surface data and cifti files. See all of the available workbench commands here https://www.humanconnectome.org/software/workbench-command/-cifti-create-dense-timeseries
Connectome wb_view is a GUI for visualization surface data, which can be downloaded here https://www.humanconnectome.org/software/get-connectome-workbench. To visualize surface data in workbench, you must load a .surf.gii surface geometry first, and then your surface data