Hi Doug,

I think I find out where the problem is. Actually the mri_vol2surf works nicely (and it's also true that tksurfer with -mni152reg samples the overlay to the white surface by default instead of to the pial surface.)

The problem is in freeview + rh.aparc.annot.

If you do the following for the attached rh mgh file, you will see it correctly displayed:

tksurfer fsaverage rh inflated -overlay rh.pial_surface.mni305.mgh

If you overlay this mgh in freeview with rh.inflated surface, but without loading rh.aparc.annot, it also displays correctly.

However, once I load the rh.aparc.annot, I start to see something very weird...

Thanks!
Daniel


-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 10/1/13 6:11 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:

I don't understand what you mean by a "much smaller brain". Can you
elaborate?
On 10/01/2013 06:10 PM, Yang, Daniel wrote:
Hi Doug,

I understand. But the end product turned out to be a much smaller
brain … so I thought there is something wrong. What should I do here?

Thanks!
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 10/1/13 6:00 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu


     The way the software is set up, you should use mni152.register.dat
     with
     mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305)
     surfaces

     doug


     On 10/01/2013 05:49 PM, Yang, Daniel wrote:

         Hi Doug,

         Just checking again, because I haven't heard from you. So the
         purpose
         is to use mri_vol2surf is convert MNI152 to a FreeSurfer
         (MNI305) mgh
         file. I am not sure about the correct register.dat to use. The
         mni152.register.dat is for MNI305 -> MNI152 though.

         I'm assuming that there exists some sort of inverse
         mni152.register.dat somewhere?

         Thanks!
         Daniel
         --
         Yung-Jui "Daniel" Yang, PhD
         Postdoctoral Researcher
         Yale Child Study Center
         New Haven, CT
         (203) 737-5454

         On 9/27/13 6:44 AM, "Yang, Daniel" <yung-jui.yang@yale.edu
         <mailto:yung-jui.yang@yale.edu%3E>> wrote:

              Thanks Doug!

              Because it maps from a MNI152 space to the FreeSurfer average
              space, do you know what register.dat I can use?

              Is it some sort of inverse mni152.register.dat?
              Thanks!
              Daniel

              --
              Yung-Jui "Daniel" Yang, PhD
              Postdoctoral Researcher
              Yale Child Study Center
              New Haven, CT
              (203) 737-5454

              On 9/26/13 12:26 PM, "Douglas N Greve"
              <mailto:greve@nmr.mgh.harvard.edu>
         <mailto:greve@nmr.mgh.harvard.edu%3E>> wrote:

                  They might be sampling to different surfaces. To make
         sure
                  they show the
                  same exact thing, try mapping the data to the surface
         with
                  mri_vol2surf
                  doug
                  On 09/25/2013 08:31 AM, Yang, Daniel wrote:

                      Dear FreeSurfer Experts,

                      I am trying to visualize fMRI activation
         (generated from
                      fsl) on the
                      fsaverage inflated surface, using
         mni152.register.dat.

                      It's odd that I find the results to be slightly
         different
                      between
                      tksurfer and freeview. However, I made sure that I am
                      using the same
                      threshold...

                      Judging from fslview, I think the result with
         freeview is
                      more
                      accurate -- is it due to tksurfer loading orig.mgz by
                      default, and
                      free view loading something else?

                      Thanks!
                      Daniel

                      --
                      Yung-Jui "Daniel" Yang, PhD
                      Postdoctoral Researcher
                      Yale Child Study Center
                      New Haven, CT
                      (203) 737-5454


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                  --
                  Douglas N. Greve, Ph.D.
                  MGH-NMR Center
                  Phone Number: 617-724-2358
                  Fax: 617-726-7422

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     --
     Douglas N. Greve, Ph.D.
     MGH-NMR Center
     Phone Number: 617-724-2358
     Fax: 617-726-7422

     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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