I think this scenario applies to you (just use your structural instead of orig.mgz). doug
-------------------------------------------------------------- I have a CRS from a voxel in my functional/diffusion/ASL/rawavg/etc "mov" volume and want to compute the CRS for the corresponding point in the orig.mgz:
origCRS = Torig * inv(Reg) * inv(Tmov) * [movC movR movS 1]' Torig: mri_info --vox2ras-tkr orig.mgz Tmov: mri_info --vox2ras-tkr mov.nii Reg: register.dat tkregister2 --mov mov.nii --reg register.dat
Test: click on a point in tkmedit very close to the left hemi white surface. Use the "Functional Overlay Index Coordinates" to compute origCRS (round to the nearest integer). Compare origCRS to the "Volume index". Note: you may need to use the "Volume RAS" from tkmedit in the computation above to get an exact match.
--------------------------------------------------------------
On 05/17/2012 05:43 AM, Sinem Burcu Erdoğan wrote:
Dear Freesurfer Community;
I need to find the corresponding voxel in a functional image for a specific structural image voxel after coregistering two images. My structural image has 256*256*125 voxels and the functional image has 64*64*30 voxels.
I use the following command
tkregister2 --s subjectname --targ structural.nii --mov functional.nii --regheader --reg directorythatyouwanttosaveregisterfile/MYregister.dat
Where the target is structural image and movable is the functional image
then click save to get MYregister.dat.
then take the inverse of the matrix
save it as invMYregister.dat, and try to use this matrix to transform from
anatomical to functional.
However; as an example when I try to map voxel (169 , 62 ,35) of the anatomical image to the functional space using the inverse registration matrix; i get the values below
- 64.3319
-146.4394
-157.2665
as the corresponding voxels' coordinates at the functional space which is far beyond the functional volume size and is negative. It is clear I cannot manage to use the trasfer matrices appropriately.
Your help will be greatly appreciated.
Thank you;
Sinem Burcu ERDOGAN
-- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdogan@boun.edu.tr mailto:burcu.erdogan@boun.edu.tr
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