How to extract cortical thickness from fsaverage space to fsLR_den-91k sapce?

[ly6ustc]

Hi,
I want to get the cortical thickness of fsLR_den-91k space from the results of fmriprep. And I want to make this process consistent with what BOLD image did, i.e., “–cifti-output”. It appears that fmriprep use “wb_command -metric-resample” to resampe fsaverage to fsLR. But I want to know more details. So I wrote my code here, if anyone could confirm it or give me some suggestions?

First I resample the thickness file (i.e.,lh.thickness in Freesurfer output directory) from native space to fsaverage164k space, like this:
mri_surf2surf --srcsubject sub-F001 --trgsubject fsaverage --hemi lh --sval /home/z/DataStorage/XW/fMRIprep/fmriprep/freesurfer/sub-F001/surf/lh.thickness --tval /home/z/DataStorage/XW/fMRIprep/fmriprep/space-fsaverage_hemi-L.thickness.func.gii

After that, I had gotten the thickness file named space-fsaverage_hemi-L.thickness.func.gii in fsaverage space.

Second I want to resample this file to fsLR_32k space, like this:
wb_command -metric-resample space-fsaverage_hemi-L.thickness.func.gii $current_sphere_L $target_sphere_L ADAP_BARY_AREA space-fsLR32K_hemi-L.thickness.func.gii -area-metrics $current_area_L $target_area_L

I don’t run this code, because I could not confirm these necessary files including $current_sphere_L, $target_sphere_L, $current_area_L, and $target_area_L.

In my opinion, for $target_sphere_L , $target_area_L are files in fsLR32K, $current_sphere_L and $current_area_L, could I use the files in the yellow lines in the screenshot below?

Besides, are there other parameters that should be added in command “wb_command -metric-resample”? e.g., the flag [-largest].

Can someone give me some suggestions or know the specific commands of fmriprep?

Thanks a lot!

[ly6ustc]

There are our cortical thickness results, left is native space, the middle is fsaverage(164k) space, and right is fsLR32K space. They look very similar, maybe my code is right?
And is normal that the results are similar between native and standard space? I think they should do some warp transformation.

[ly6ustc]

But I found if using the “mri_surf2surf” as mentioned, would yield some vertices with value in the medial wall such as the left figure below, so I add “–cortex” when I used the “mri_surf2surf”, generating better results(right figure).

[ly6ustc]

According to the code mentioned above (I think the most suitable code), the result is still somewhat different from the result of fmriprep. As shown in the figure below, the left side is the result of our cortical thickness, and the right side is the result of fmriprep’s BOLD preprocessing, both in fsLR32k Space, but our result seems to have eroded a few vertices towards the medial wall. Or just ignore these vertices?