Re: [Freesurfer] Alignment to ACPC

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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:

...

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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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