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By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat file, I can fix the issue. But I would still appreciate any suggestions on how to use mri_vol2vol with a binarized mask, or what might be causing the system to fill the whole volume.

Best

Idil

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From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yagmur Ozdemir 19 [yozdemir19@amherst.edu]
Sent: Tuesday, July 24, 2018 1:23 PM
To: Freesurfer support list ‎[freesurfer@nmr.mgh.harvard.edu]‎
Subject: [Freesurfer] tkregister2 scripting- help with saving reg.dat

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Hello freesurfer experts,

I am editing the registration matrix between two volumes (fsaverage's T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the registration because I do not have permission to change the .dat file I originally opened with tkregister2. I cannot change the permissions. I do not want to lose all the editing I have done so far, so would really appreciate if someone could give me advice on how to save the registration as a seperate file either in GUI or from terminal.

FYI, I know ideally I shouldn't need to edit the registration but for some reason I had weird flipping issues when using mri_vol2vol and mni152.register.dat with --inv option. Also the system for some reason does not recognize a binary volume with the --interp nearest option, so fills in the whole volume. I would appreciate any suggestions.

Best

Idil

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