Re: [Freesurfer] Alignment to ACPC

Hi Sadia

the only way to confirm it is to visually inspect it.

cheers Bruce On Tue, 26 Feb 2019, Sadia Sheikh wrote:

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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:

  >
  >         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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