hi bruce, the mask was generated by morphing a binary mask from CVS space back to the subject's anatomical space. the cvs mask was generated from a functional parcellation algorithm our lab uses.
if it's useful -- the registration header in the anatomical-space mask is identical to the orig.mgz's. alex On Fri, Aug 17, 2012 at 11:07 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > 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 >> >> > > 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<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. > >
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