GongZhengxin
commented
6 months ago Hi, sorry for the late,
Why is the size 59k? Referring to this paper (The minimal preprocessing pipelines for the Human Connectome Project - ScienceDirect), it is mentioned in the caption of Fig. 1:
Left and right cerebral cortices contribute about 30k surface vertices each (less than the 32k vertex standard meshes, because the non-cortical medial wall is masked with standard ROIs).
In other words, vertices from the inner sides of both hemispheres (which include the corpus callosum and ventricles, as I understand) are excluded in the indexing, resulting in a total of 59k vertices remaining in the cortex.
How to determine the relationship between cifti indices and surface vertices?
In the fsLR32k space, each hemisphere has 32,492 vertices, and data with this shape is typically stored in Gifti format (.gii). For files like .dtseries.nii / .dlabel.nii / .dscalar.nii, you can use nibabel to retrieve vertex information from the header. Please refer to the attached code for specific implementation details
. If you are familiar with R, this package might be very convenient for handling cifti files (Unfortunately, I am not proficient in R).
Hi Gongzheng,
It is great work and a nice dataset, but I had a few questions regarding ciftify results. I am not very familiar with this toolbox, so correct me if I were wrong.
In "derivatives/ciftify/sub-XX", we got all surface mesh as ".surf.gii", they were in 32k vertices and stored according to left and right hemisphere respectively. However, all the "dlabel.nii" label file and fMRI beta results were in size of 59k, and got no splition for left and right hemisphere.
Is there any transformation between the 32k+32k surface mesh towards the 59k labels and results?
Regards.