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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: 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: 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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