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
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:
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
-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:
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
|
Sender notified by Mailtrack | 23/08/13 12:20:38 |
