thanks a bunch for your guys' help!

alex

On Fri, Aug 17, 2012 at 2:30 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Ah, I did not see that you had used inflated in your original vol2surf command. That is definitely the source of the misplaced label. The surf_name.mgz file is not a surface, it is an overlay. If you are trying to load it as a surface in tksurfer (or getting info from mris_info), then it will try to read it as a surface and fail. To look at it in tksurfer, load it as an overlay, eg tksurfer subject lh inflated -overlay surf_name.mgz

doug

On 08/17/2012 02:26 PM, 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 failed
No 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 <greve@nmr.mgh.harvard.edu <mailto:greve@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
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