External Email - Use Caution
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
[image: Mailtrack] https://secure-web.cisco.com/1FgOh-kgul0oJnTKW_HJ-Y6578cTV4_OlVhajI96G-Utzr00Twuhnw4oKa2Ali3CfayWwziBPMVs9LdNjpHl9CyJbJQJrqXJWloA8mTco-RLn-iXnb4R1BOtp4Uuu70JP2kXRsCklY4OxQvL_hvvYb3vExplx6tb-cea_Bz8kUYYlrx-UzcUTadZzi8r3u_pJpZpJvJ-qeiAenfz42xuBcYSVnGGEwzRTLnfic7PZv_5dFxnwnuhw99lBeA5IVnPqsPDMMFMxFoEJTDkaSa9gAe-MDTu3xB67ZoZdjC4aknSSvONk7C3RPkVGuUOtkva7snm7_aI-7aYJlz_zYO714w/https%3A%2F%2Fmailtrack.io%3Futm_source%3Dgmail%26utm_medium%3Dsignature%26utm_campaign%3Dsignaturevirality11%26 Sender notified by Mailtrack https://secure-web.cisco.com/1FgOh-kgul0oJnTKW_HJ-Y6578cTV4_OlVhajI96G-Utzr00Twuhnw4oKa2Ali3CfayWwziBPMVs9LdNjpHl9CyJbJQJrqXJWloA8mTco-RLn-iXnb4R1BOtp4Uuu70JP2kXRsCklY4OxQvL_hvvYb3vExplx6tb-cea_Bz8kUYYlrx-UzcUTadZzi8r3u_pJpZpJvJ-qeiAenfz42xuBcYSVnGGEwzRTLnfic7PZv_5dFxnwnuhw99lBeA5IVnPqsPDMMFMxFoEJTDkaSa9gAe-MDTu3xB67ZoZdjC4aknSSvONk7C3RPkVGuUOtkva7snm7_aI-7aYJlz_zYO714w/https%3A%2F%2Fmailtrack.io%3Futm_source%3Dgmail%26utm_medium%3Dsignature%26utm_campaign%3Dsignaturevirality11%26 23/08/13 12:20:38
External Email - Use Caution
Try mri_convert brainmask.mgz -at transforms/talairach.xfm.lta align.mgz
On 8/13/2023 12:25 AM, QL X wrote:
External Email - Use Caution
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.mgzThis 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.mgzBut 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
Mailtrack https://secure-web.cisco.com/1FgOh-kgul0oJnTKW_HJ-Y6578cTV4_OlVhajI96G-Utzr00Twuhnw4oKa2Ali3CfayWwziBPMVs9LdNjpHl9CyJbJQJrqXJWloA8mTco-RLn-iXnb4R1BOtp4Uuu70JP2kXRsCklY4OxQvL_hvvYb3vExplx6tb-cea_Bz8kUYYlrx-UzcUTadZzi8r3u_pJpZpJvJ-qeiAenfz42xuBcYSVnGGEwzRTLnfic7PZv_5dFxnwnuhw99lBeA5IVnPqsPDMMFMxFoEJTDkaSa9gAe-MDTu3xB67ZoZdjC4aknSSvONk7C3RPkVGuUOtkva7snm7_aI-7aYJlz_zYO714w/https%3A%2F%2Fmailtrack.io%3Futm_source%3Dgmail%26utm_medium%3Dsignature%26utm_campaign%3Dsignaturevirality11%26 Sender notified by Mailtrack https://secure-web.cisco.com/1FgOh-kgul0oJnTKW_HJ-Y6578cTV4_OlVhajI96G-Utzr00Twuhnw4oKa2Ali3CfayWwziBPMVs9LdNjpHl9CyJbJQJrqXJWloA8mTco-RLn-iXnb4R1BOtp4Uuu70JP2kXRsCklY4OxQvL_hvvYb3vExplx6tb-cea_Bz8kUYYlrx-UzcUTadZzi8r3u_pJpZpJvJ-qeiAenfz42xuBcYSVnGGEwzRTLnfic7PZv_5dFxnwnuhw99lBeA5IVnPqsPDMMFMxFoEJTDkaSa9gAe-MDTu3xB67ZoZdjC4aknSSvONk7C3RPkVGuUOtkva7snm7_aI-7aYJlz_zYO714w/https%3A%2F%2Fmailtrack.io%3Futm_source%3Dgmail%26utm_medium%3Dsignature%26utm_campaign%3Dsignaturevirality11%26 23/08/13 12:20:38
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Douglas N. Greve -
QL X