Hi Doug,
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz
tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg register.dat
mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native --tval-xyz --hemi lh --s 1158119_3_6
For the previous snapshot, I ran FreeView, and loaded volume and surface using mouse/menu selection.
I just ran
freeview -v brain-in-rawavg_tb.mgz -f lh.pial.native
with snapshot attached.
-Tim
On Fri, 8 Mar 2013, Douglas N Greve wrote:
Tim, what were your vol2vol, surf2surf, and freeview commandlines? doug On 03/08/2013 11:10 AM, Timothy Brown wrote:
Hi Doug,
Thank you for your reply.
I tried FreeView and have attached screenshots of results.
freeview_native_brain.jpg - snapshot of native brain
freeview_aseg.jpg - aseg.mgz added. This appears to correspond with native brain
freeview_aseg_in_raw.jpg - aseg_in_raw shown. This is quite similar to aseg.mgz. Slightly different, as I'd expect, corresponds well to native brain.
freeview_native_brain_lh_pial.jpg - The pial (left) surface is shown. This is the FreeSurfer output, ie not reoriented. It corresponds well to aseg.mgz and native brain
freeview_native_brain_lh_pial_native.jpg - The pial (left) surface that I created using register.dat and mri_surf2surf is shown. This does not correspond to the native brain.
I wonder if there are some FreeView options that I should be using?
Best regards, -Tim
On Thu, 7 Mar 2013, Douglas N Greve wrote:
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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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
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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
