Your best bet is to use tkregister2 and mri_vol2vol, something like:
tkregister2 --targ orig --mov dicom --regheader --reg register.dat
where orig is the freesurfer orig volume and dicom is your original
dicom (or some other format that has the orginal
geometry). tkregister2 will bring up a window in which you can edit
the registration (hopefully this won't be necessary). Save the
registration matrix, then run mri_vol2vol, something like:
mri_vol2vol --in orig --out orig.dicomspace.img --temp dicom --xfm register.dat
run either of these commands with --help to get help
doug
On Tue, 13 Sep 2005, Bakkour, Akram wrote:
Dear all,
I am an undergraduate student working in Dr. David Ress' lab at Brown
University making a comparison of different brain segmentation applications
among them freesurfer.
However, I ran into much difficulty conducting a proper quantitative comparison
of outputs. Indeed, I noticed that the data was shifted and possibly rotated in
freesurfer.
In order to superimpose the output by the different applications I must put all
data back in its original coordinate system.
I was wondering if there is a way of obtaining the transformation matrix used
by freesufer.
Thank you very much for your help.
My very best regards,
Akram.
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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