-----Original Message-----
I have a text file with list of native space voxel-coordinates for which
I
want to know the position in standard space. I have warped whole brain
images from native to standard space and have obtained the
parameter-file
from the spm_normalize procedure.
I am particularly unsure about the non-affine part.
---------------------------
If you want to obtain this info, then you'll need to write out the
inverse of the deformation field encoded in the sn.mat file.
Select TASK->Util->Deformations from the pulldown in the Graphics window
of SPM5. Then fill in the appropriate fields:
-Deformations
-Composiotion
-Inverse
-Composition
-Imported _sn.mat
Parameter File: This is your sn.mat
Voxel Sizes: leave at default values
Bounding Box: leave at default values
Image to base inverse on: Your native space image
Save as: Give it a filename
Apply to: Leave blank, unless you want one of the MNI space
images warped to match the native space image.
Then you can simply read out the values from the deformation field you
generated. E.g. for reading voxel 20,30,40 you could use:
P=spm_select(1,'nifti','Select the image');
N=nifti(P);
Dat = N.dat;
squeeze(Dat(20,30,40,:,:))
All the best,
-John
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