External Email - Use Caution        

Thanks for your response Sir 

I did that using mri_convert for the orig.mgz file and brainstem segmented file. 
(mri_convert orig.mgz --apply_transform transforms/talairach.xfm -o orig.talairach.mgz). but the image doesn't seem like to be aligned.
How can I confirm that the image is ACPC aligned or not and how is the transformation matrix in transforms.xfm file is evaluated.

Thanks in advance
Sadia

On Sat 23 Feb, 2019, 12:38 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu wrote:
Hi Sadia

we don't align to AC-PC, but we do compute a talairach transformation in
$SUBJECTS_DIR/$subjects/mri/transforms/talairach.xfm that should do so. You
can apply it using mri_convert or mri_vol2vol.

cheers
Bruce

On
Fri, 22 Feb 2019, Sadia Sheikh wrote:

>
>         External Email - Use Caution        
>
> Hello Freesurfer experts
> Freesurfer preprocessed data by(recon-all) are ACPC aligned?
> If not how can I align my files to ACPC? I read the documents but I am still very confused about the
> alignment and coordinate system in freesurfer.
>
> Thanks in advance
>
> Regards
> Sadia
> Research Student
>
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