Ugh, that's weird, I don't know what's going on with that. I'll have to
dig into it more.
On 1/27/15 1:26 PM, Benjamin Zimmerman wrote:
Hello,
When I try your recommended code, I am able to get the data back into
volumetric space, but one hemisphere's cortex is significantly thinner
than the other. If I do mri_surf2vol separately on each hemisphere, I
don't have this problem. It seems to occur only if I try merging the
two files. I assume that this is because I am using the volume that I
am merging to as a template instead of inputting the template
directly. Do you have any ideas how to solve this problem?
Thanks for your help,
Ben
On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
I don't think we have a tool to display the color wheel in a
volume. FreeView might be able to do it. For the color wheel in
tksurfer, you are looking at the angle file (one for eccen and one
for polar), so you would map them. You can run mri_surf2vol
something like
mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject
--hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz
mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject
--hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz
doug
On 12/18/14 1:24 PM, Benjamin Zimmerman wrote:
I mean the individual's anatomical volumetric space.
On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
What do you mean by the individual's volumetric space? The
anatomical
space or the functional space?
On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote:
> Thanks for the advice. I thought I would like to use
mri_surf2vol, but
> I am a little confused about the parameters and how they
relate to
> what the retinotopy analysis outputs.
>
> To be explicit, I want to view the real.nii.gz and
imag.nii.gz files
> in an individual's volumetric space. I can load these as
overlays to
> the inflated surface using tksurfer <subject> <hemisphere>
inflated.
> Then I can configure the overlay to use a color wheel color
scale and
> display as complex to see the retinotopic mapping.
>
> I'm not sure how I would go about using mri_surf2vol to
recreate this
> map in volumetric space. Should I just use real.nii.gz and
imag.nii.gz
> as surfval? Where is the registration file outputted in a
retinotopy
> analysis?
>
> Thank you for any more help that you can provide,
>
> Ben
>
> On Mon, Dec 15, 2014 at 3:26 PM, dgw <dgwake...@gmail.com
<mailto:dgwake...@gmail.com>
> <mailto:dgwake...@gmail.com <mailto:dgwake...@gmail.com>>> wrote:
>
> Hi Ben,
>
> You should be able to map it back with mri_surf2vol. I
haven't done
> this, but the wiki page looks fairly detailed:
> http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol
>
> HTH
> D
>
> On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman
> <benjamin.zimmerm...@gmail.com
<mailto:benjamin.zimmerm...@gmail.com>
> <mailto:benjamin.zimmerm...@gmail.com
<mailto:benjamin.zimmerm...@gmail.com>>> wrote:
> > Hi all,
> >
> > FsFast has an excellent individual retinotopy
analysis that
> allows me to see
> > phase data on the inflated surface of the brain. Is
there a way
> to view the
> > results of the retinotopy analysis in the subject's
original
> volumetric
> > space rather than on the subject's surface space?
> >
> > Thank you for any help,
> >
> > Ben
> >
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