Dear @Antonin_Skoch,
Thanks for being so detailed in your explanations of how to do this - I managed to map the cortical labels onto the volume-based segmentation file successfully.
Before I rerun parts of my analysis, I’d like to clarify with regard to the T1w_acpc_dc_restore_brain.nii.gz within the HCP subject 100307’s T1w folder. In the tutorial, it states that we could just run 5ttgen on this file. However, I understand from other threads that we would need the T1 to be transformed to diffusion space before running 5ttgen. However, when I checked, this file’s pixel dimensions are 0.7x0.7x0.7mm whereas the data.nii.gz (diffusion image file) has pixel dimensions of 1.25x1.25x1.25mm. Is this right, or am I using the wrong files to follow the tutorial? The aparc+aseg.nii.gz file also follows 0.7x0.7x0.7mm.
Side note: There is also another T1 file called T1w_acpc_dc_restore_1.25.nii.gz within the diffusion folder that has not been through skull strip. The pixel dimensions for this file is 1.25x1.25x1.25.
I guess it’s a little confusing both because the HCP data folder contains varying files that are similar, and in the tutorial it states “Note that it is not necessary to use a tissue-segmented image that has the same resolution as the diffusion images”. Thus it’s a little confusing whether registration and transformation to diffusion space is needed?
Thanks, I really appreciate your help! Maybe some others who wrote the tutorial can chime in as well.
Best wishes,
M.