Try adding -oc 0 0 0 to the mri_convert command line

On 9/28/2020 12:55 PM, Yi Li wrote:

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Hi Douglas,

I ran mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.talairach.mgz

But brainmask.talairach.mgz is all black. No error was thrown during talairach transformation computation. Could you help to check what’s going on here? I attached 4 relevant files in the mail.

Thanks and best regards,

Yi

*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, September 15, 2020 1:33 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation

Try mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz

On 9/15/2020 1:24 PM, Yi Li wrote:

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Is there command in freesurfer that applies the linear transform
(I suppose talairach.xfm) to brainmask.mgz to get the registered
image?

Best,

Yi

*From:* freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of
*Douglas N. Greve
*Sent:* Tuesday, September 15, 2020 1:20 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [EXTERNAL]Re: [Freesurfer] a question on Talairach
transformation

No, it is in native individual space. We compute a linear
transform but do not apply it

On 9/15/2020 1:07 PM, Yi Li wrote:

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    Hi,

    I am a beginner of Freesurfer. I would be grateful if you
    could help me understand the excellent software.

    I got brainmask.mgz at the end of autorecon1 and brain.mgz in
    the middle of autorecon2. Are these the images registered to
    MNI305 template?

    In other words, is my understanding correct that brainmask.mgz
    is the image after orig.mgz is linearly registered to MNI305
    (plus normalization and skullstripping), while brain.mgz is
    the image after normalized image is nonlinearly registered to
    MNI305 (plus cropping based on brainmask.mgz and further
    normalization)?

    Thank you so much for your help in advance.

    Best regards

    Yi Li

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