i don't really use tkmedit. with freeview it's right where it should be -- e.g., see attached.
alex
On Fri, Aug 17, 2012 at 11:43 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
does it align with say the orig.mgz when viewed in tkmedit?
On Fri, 17 Aug 2012, Alex Kell wrote:
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 < fischl@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. alexThe 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/**compliancelinehttp://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.
