That will go to mni305 space. Is that the same as collin space? In general, you can just:

bbregister --init-fsl --mov collinsbrain.nii --s $subject --t1 --reg reg.$subject-to-collin.dat

where $subject is the name of your subject. Then

mri_vol2vol --reg reg.subject-to-collin.dat --targ $SUBJECTS_DIR/$subject/mri/brainmask.mgz --mov collinsbrain.nii --inv --o subject-in-collin.nii --interp nearest

Bruce Fischl wrote:

mri_convert -at <tal.xfm> <in volume> <out volume>

make sure you use -rt nearest for the sagmentation volume to avoid trilinear interpolation. <tal.xfm> should be the talairach.xfm in the subject's transforms dir.

cheers Bruce

On Wed, 21 Oct 2009, Gabriel Go.Es. wrote:

...

Hello

i have a question i want to convert an MRI subject (brainmask.mgz in talairach apace) and a mask of subcortical structure of the same subject, from freesurfer to MNI colins space to work with SPM5, how can i make it?

and in fact i need to make this transformation to a set of subjects.

any help will be so appreciated

Best Regards

Gabriel

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