Hi Shani, it looks like your commands are right. How are you judging that the mask is thicker? What is the resolution of the DTI volume? When you binarize in a coarser space, you'll naturally not get it to line up with the surface, and the binary mask will naturally be thicker. doug
On 02/21/2013 08:22 AM, Shani Ben Amitay wrote: > Dear freesurfers > > I'm using bbregister and mri_surf2surf to transform intermediate > cortical surfaces and mid surfaces normals to diffusion space. > Next I'm trying to generate volumes from these surfaces (in the same > diffusion space), however the generated volumes are much thicker then > the generated surfaces. > for example to generate surface normals I used the following: > mri_surf2surf --s subjectid --hemi lh --sval-nxyz > white_surface_in_diffusion --tval lhwhitediffusion_n.mgh > mri_surf2vol --surfval lhwhitediffusion_n.mgh --hemi lh --surf white > --reg mri/register.dat --outvol lh_white_n.img --template lowb.img > Any idea what am I doing wrong? > > Thanks! > > Shani > > > _______________________________________________ > 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
