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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
[X]
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[dgr...@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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
on behalf of Yagmur Ozdemir 19
[yozdemi...@amherst.edu<mailto:yozdemi...@amherst.edu>]
Sent: Tuesday, July 24, 2018 1:23 PM
To: Freesurfer support list
[freesurfer@nmr.mgh.harvard.edu<mailto: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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