Re: [Freesurfer] Affine Transform to Talairach Failed

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Try mri_convert brainmask.mgz -at transforms/talairach.xfm.lta align.mgz

On 8/13/2023 12:25 AM, QL X wrote:

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Dear list:

I want to use freesurfer to do the preprocess, transform the image to Talairach space. I use the |recon-all| command with |autorecon1| and obtain the talairach.xfm file. Then I use mri_convert with |--apply_transform| option. Here's the code I used:

recon-all -parallel -i $sample_path -autorecon1 -subjid $sample_name 
-cw256
mri_convert --apply_transform mri/transforms/talairach.xfm \
mri/brainmask.mgz \
mri/brainmask_align.mgz

This operation moves the brain outside of the image boundary: image.png

I also tried this which is suggested by freesurfer mri_convert documentation:

mri_convert --apply_transform mri/transforms/talairach.xfm \
-oc 0 0 0 \
mri/brainmask.mgz \
mri/brainmask_align.mgz

But the brain shape is weird and still some part of it is out of boundary: image.png

I'm not sure why this happens. I didn't notice any errors when using autorecon1 command. I have checked recon_all.log and the program finished without error.

What should I do to transform the image to Talairach space correctly?

Looking forward to your reply.

Best regards,

gyddhpy

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