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 > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
