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.edu> wrote:
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.


            alex



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