Hi Alex when you say it is in the native anatomical space can you elaborate? How did you create the mask?
Bruce On Fri, 17 Aug 2012, Alex Kell wrote: > hi freesurfers, > > i'm trying to move a volume from a subject's native anatomical space > to that subject's surface space, and i'm running into some difficulty. > > we have binary masks in each subject's native anatomical space and > we'd like to move these to be labels in that subject's surface space. > there we'd edit them (either manually or with dilation and erosion) > and extract some simple anatomical measures (like thickness) from that > region in the surface space. to do this, i am using mri_vol2surf to > get the volume in the subject's surface space, and then using > mri_cor2label to convert this surface file to a label. the problem is > that when i look at the label in the surface space, it is in clearly > the wrong position -- even though when i look at the volumetric mask > as an overlay in tksurfer it looks like it's in the position that it's > supposed to be. for instance, see the attached. magenta is the > volumetric mask overlay (in the correct position) and the blue-red > circle is the label file (in the wrong position). > > my calls: > > mri_vol2surf --mov <volumetric_mask> --reg identity.dat --hemi rh > --inflated --o <output_surf_file> > mri_cor2label --i <output_surf_file> --id 1 --l ./<surf_label> --surf > <subj> rh inflated > > "identity.dat" is a tkregister-style registration matrix where i just > put ones on the diagonal and zeros everywhere else. i also tried > mri_vol2surf where i used the --regheader flag. > > any thoughts? what's going on here? > > thanks in advance. > > > alex > _______________________________________________ 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.
