It may be that the registration is off. You should load your gm volume with the surfaces on top, something like
tkmeditfv -f orig.mgz -aux gm_values2anat.nii -surfs On 12/06/2016 01:41 PM, Ilaria Mazzonetto wrote: > > Hi Freesurfer User, > > I would like to map a volume to a surface. I have a T1 image (SubjX) > with resolution 1x1x1 and a gray matter mask with resolution 6x6x6. > The voxels in the lower resolution image (gm_values.nii) have zero > value if they are not in the gray matter and a value between 0.1 and > 20 if they are in the gray matter. What I want to do is mapping this > values in the pial surface. I runned recon-all with T1 image and I > coregistered the lower resolution image (the mask) to higher > resolution image with FSL (gm_values2anat.nii). Then I runned > mri_vol2surf -- src gm_values2anat.nii --regheader SubjX --hemi lh > --surf pial --o gm_values_lhsurf.mgh. I do not understand what the > options for surface normal projection mean. I inspected the result > with tksurfer, setting fminmask 0 20, and there are a lot of holes. > > Do you think there is something wrong in what I did? > > Any help would be greatly appreciated. > > Regards. > > Ilaria > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] 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.
