Hi Yuanchao, I would recommend that you use the aparc+aseg.mgz file for this. This file has cortical labels already in the volume, you just need to map them to your functional space, something like

mri_label2vol --aparc+aseg --temp functemplate.nii --reg register.dat --o aparc+aseg.fmri.nii

doug

Zhangyuanchao wrote:

hi, expert,

By mapping a surface label to a functional template, I want to extract the corresponding cortical gray matter region in the functional space. I know I should use the mri_label2vol command.

In the help page of mri_label2vol, I see some examples of this command.

2. Convert a surface label into a binary mask in the functional space.

Fill in all the cortical gray matter. Require that a functional voxel be filled at least 30% by the label:

mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject bert --hemi lh --o cent-lh.nii

3. Convert a surface label into a binary mask in the functional space.

Sample a 1mm ribbon 2mm below the gray/white surface. Do not require a fill threshold:

mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii --reg register.dat --proj abs -3 -2 .1 --subject bert --hemi lh --o cent-lh.nii

I want to extract the cortical gray matter on the functional images corresponding to the surface label. I do not know which of the above commands could obtain the result I want and which parameters I should use to obtain what I want.

For example 3, I do not quite catch what "Sample a 1mm ribbon 2mm below the gray/white surface. " this sentence means.

Thanks for your help!

Best

Yuanchao

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