Thanks Doug...I was also wondering if it were possible to load our own overlays on the surface (eg. pial surface)?

Would this be done using tksurfer or would some other program/command be needed?

Thanks.

Adam

Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

I think I see what you mean. But the answer is no, FreeSurfer will always resample to 256^3, 1mm, coronal. But you  can still use your ROIs, you just need to make a registration matrix first. Do this:

tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat

It is assumed that rawavg.mgz is in the native space (same

This will bring up a window with a control panel. Hit the Compare button. The two images should be identical. Look at a few slices/orientations to assure this. Hit the Save Reg button -- this creates register.dat

Then run mri_vol2vol. I've recently modified it and you might not have the most recent version, so I've copied it here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol

specify your roi volume as the --mov and use nearest neighbor interp

doug




adam walczak wrote:

Doug,

I think that you answered my question.  We wanted to
overlay some ROI files onto the freesurfer created
surfaces, but the ROIs were made before we ran the
images through freesurfer.  So we wanted to make sure
that we could keep the surfaces in the same space as
the ROIs we
 created...is that an answer to your
question?

Adam

--- Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

  

What do you mean by "native space"? The
reconstruction is not done in 
tal space.

doug

adam walczak wrote:

    

Hello,

I want to make cortical surface images that we
      

will overlay with our 
    

own masks.  But we want to do this in native
      

space.  So, I was 
    

wondering if it is possible to go thorugh the
      

reconstruction process 
    

to make the surfaces without ever using the
      

talairach transform and 
    

keeping everything in its native space.

Thank you,

Adam


adam


      

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-- 
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

    

adam

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting