Definitly do not use --rot 180. I think the registration matrix goes in the other direction, so try adding --inv to the command line and changing --targ and --mov

On 7/25/18 8:24 PM, Sims, Sara A wrote:

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Hello,

I am trying to put a mask that I made on the MNI brain (that had been run through recon) into individual subject space. I have already created a registration matrix using the following command:

mni152reg --s $patient --o $registration/$patient/registermni_$patient.dat --1 --save-vol

Now I want to apply this matrix but from MNI -> subject. So I tried doing this:

mri_vol2vol --targ $patient/mri/orig.nii --mov $mnimask/net4splitmask_bin.nii --reg $registration/$patient/registermni_$patient.dat --o $outp/$patient/net4splitmask_bin.nii --nearest --rot 180 0 0

But it just spits back out the MNI mask ($mnimask/net4splitmask_bin.nii) in MNI space. I tried using -inv but realized that was wrong because then it just gave me the subject’s orig. How can I get it to actually put the MNI-space mask onto the subject’s brain?

Sara

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