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I am using mri_vol2vol --mov L_AIP_mask.nii.gz --targ $FSLDIR/standard/MNI152_T1_1mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.mni305.subfov1.dat --o L_AIP_MNI152.nii.gz --interp nearest

(I used mni152.mni305.subfov1.dat in my registration of T1.mgz into MNI152 space, at the time mni152.register.dat created weird flipping problems, so I am using it here as well)

So when I check this in freeview it paints the whole brain and I see that the file is not binarized. I attached a picture, the brain under is the adjusted MNI152 T1 which I corrected manually.

I also tried this:
mri_label2vol --seg L_AIP_mask.nii.gz --reg $FREESURFER_HOME/average/mni152.mni305.subfov1.dat --invertmtx --o L_AIP_MNI152.nii.gz
And it created a binarized volume just like I wanted, but registration was way off and not possible to correct manually because the unmasked volume is so small. I tried to feed a template volume inside this and it didn't create anything.

Thank you for all the help!
Best
Idil

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [dgreve@mgh.harvard.edu]
Sent: Tuesday, July 24, 2018 5:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

no idea how to help with the vol2vol problem without a command line and more description of the problem

On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote:

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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
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 ý[freesurfer@nmr.mgh.harvard.edu]ý
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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