what is your command line? You have to load it as an overlay, it isn't a
surface just a scalar field over the surface
On Fri, 17 Aug 2012, Alex Kell
wrote:
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get
the following error messages repeatedly (like >100 times and keeps going
until i interrupt the call).
freadFloat: fread failedNo such file or directory
i tried mri_vol2surf using the white surface instead of the inflated and i
get the same fread errors.
the white call is: mri_vol2surf --mov <volumetric_mask> --regheader
<subj_id> --hemi rh --surf white --o <surf_name>.mgz
alex
On Fri, Aug 17, 2012 at 1:18 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
Hi Alex, does the output of mri_vol2surf look ok on the surface?
When
you run mri_cor2label, you should use the white or pial surface
instead
of inflated, but I don't think that is the problem here. Another
thing
to look at is
tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s
subjectname
and make sure that the label is in the right place (hit the
compare
button to flip back and forth).
doug
On 08/17/2012 11:02 AM, 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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