Re: [Freesurfer] Mapping of fsaverage surface to native volume

Hi Doug,

Again a strange result, although it now vaguely looks like a brain... see attachment. So it should be something with the integrity of the original files? Is there anything that can be done there? By the way, tkmedit didn't recognize the -fthresh option, any idea whether that is relevant? Concerning the version: >>which tkmedit displayed /opt/mumc/apps/freesurfer-5.1.0/bin/tkmedit.

Best regards,

Rene

On Tue, Apr 17, 2012 at 5:52 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

Can you run the following?

mri_surf2vol --mkmask --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o surf-mask.nii tkmedit sub01 orig.mgz -overlay surf-mask.nii -fthresh .5

this should just create a mask of the rh surface in the volume. If this fails, then there's something wrong with the subject data.

doug

On 04/17/2012 03:43 AM, René Besseling wrote:

...

That gives the same scattered appearance as before, see attachment. So I guess it's not a viewer issue. Maybe something to do with missing header information of the original T1 scan? By the way: strange that the overlay contains so many zeros; one would expect (transparent) NaNs...

Best regards,

Rene

On Thu, Apr 12, 2012 at 7:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Try loading it in tkmedit, something like:

tkmedit sub01 orig.mgz -overlay sig_2subj01_volumetric.nii

doug


On 04/12/2012 03:46 AM, René Besseling wrote:

    Hi Doug,

    Sorry, missed your reply. I assumed the --identity argument
    was used for looking up the surface-to-volume mapping
    somewhere in the predefined folder structure of this subject.
    Anyhow, my last command was
    mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon
    --identity sub01 --template subj01/mri/orig.mgz --o
    sig_2subj01_volumetric.nii
    so I guess no transformation is needed since the surface is
    already in the proper space (that of subj01).
    About my tkmedit command: I'm not using that. I usually
    visualize my results in Matlab, for the pics I send I used
    Freeview and tksurfer (so commands such as "mrview T1.mgz" and
    "tksurfer fsaverage lh inflated")
    Best regards,
    René


    2012/4/5 Douglas N Greve <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>


       The template specifies the output geometry. When you specify
       --identity, you specify a particular transformation between

the

...

       volume and the surface, so you can't change the target volume
       without specifying a different transform. I'm at a bit of a
    loss
       as to why this is not working. What is your tkmedit command?
       doug


       On 04/05/2012 06:04 AM, René Besseling wrote:

           Hi Doug,

           I'm using tksurfer to visualize the surface maps; this
    looks
           OK for both the original map overlaid on fsaverage and the
           mapped surface (generated using mri_surf2surf) overlaid on
           subj01. The mapping from surface to cortical ribbon
    also works
           well for fsaverage but goes haywire for subj01, see pics

in

...

           attachment.

           I noticed that mri_surf2vol gives different results
    when using
           different --template volumes. Why is that? I assumed
    that the
           --template image essentially provides the range of voxel
           coordinates to which the surface values can be mapped. In
           other words: when providing a template with a bigger
    field of
           view, I'd expect the center of the resulting output to

look

...

           the same as the output generating when using a small FOV
           template. Does it matter whether you write your output
    as .mgz
           or .nii?

           Best regards,

           Rene

           On Wed, Apr 4, 2012 at 10:42 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>

    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

              How are you visualizing the results? Can you send a

pic?

...

           You should be
              using tkmedit.
              doug

              On 04/04/2012 09:59 AM, René Besseling wrote:
    > Dear Freesurfer users,
    >
    > I've been trying to map a Qdec contrast sig.mgh to the
           native volume
    > of a subject using mri_surf2surf (to get from Qdec fsaverage
           surface
    > to native surface) and mri_surf2vol (to map from native
           surface to
    > native volume cortical ribbon). However, the last step goes
           wrong: I
    > get a nii with the same range of values as were in the
           surface, but
    > the nonzero voxels are scattered all over, so I guess there is
    > something wrong with the surface-to-voxel coordinate mapping.
              Below is
    > my code, any ideas on what goes wrong?
    >
    > Best regards,
    >
    > Rene
    >
    > mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape
           --sval
    > sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh
    >
    > mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon
    > --identity sub01 --template subj01/mri/orig.mgz --o
    > sig_2subj01_volumetric.nii
    >
    >
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              MGH-NMR Center
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       MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

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