Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit rigid and expects things to be a certain way (ie, not in native space). Try using freeview instead. doug

On 03/07/2013 03:19 PM, Timothy Brown wrote:

Dear FreeSurfer users,

I wish to view volumes and surfaces in native space.

I used the information at:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

to convert volumes.

I then used:

tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat cp register.dat ../surf/ mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6

When I use tkmedit to view the surfaces and volumes, the surface that I thought would be in native space does not seem to correspond with the "native space" volumes. (graphic attached)

Can you let me know the steps/procedure to do this?

Many thanks,

-Tim

Timothy Brown email: timothy@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218

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