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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
Download connectome workbench using these commands in your terminal (for ubuntu [https://neuro.debian.net/pkgs/connectome-workbench.html]; otherwise [https://www.humanconnectome.org/software/get-connectome-workbench])
Monospaced Textwget -O- http://neuro.debian.net/lists/noble.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv –recv-keys –keyserver hkps:keyserver.ubuntu.com 0xA5D32F012649A5A9
Now you can update the package index and you are ready to install packages. Simply execute the following command in a terminal:
sudo apt-get update
You are ready to go – enjoy NeuroDebian!
Note Not every package is available for all distributions/releases. For information about which package version is available for which release and architecture, please have a look at the corresponding package pages.
Step 2
To install the connectome-workbench package on your system or virtual machine, open a terminal and execute the following command:
sudo apt-get install connectome-workbench
==== wb_view ====
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. On Rhea (linux server), TemplateFlow has already downloaded some of these to /opt/ni_tools/templateflow/tpl-fsLR.
To see your files on a surface: File > Load /Volumes/Hera/Projects/Habit/mr/tpl/tpl-fsLR_den-32k_hemi-L_midthickness.surf.gii