External Email - Use Caution
Hello Freesurfer Experts, I have been trying to run mri_cvs_register to bring sub-millimeter data into MNI space, however the final outputs have large deformations to the brain. I have tried with both 0.5 mm and 0.7 mm using their respective sub-milimeter recons. It seems that the issue arises during Step 3(i) as the el_reg_tocvs_avg35_inMNI152.mgz does not have the deformations, but the step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz file does. Does anyone have any guidance on how I can troubleshoot this?
I have attached the recon-all.log file for the 0.7 mm data. If you need me to share any other files, let me know.
FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS
Thank you, Noriana Jakopin
Hi Noriana, Do you have the log file from the cvs_registration itself? I assume that the recon for your data was successful. Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Noriana Jakopin nejakopin1@gmail.com Sent: Thursday, September 3, 2020 1:45 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_cvs_register with sub-millimeter recons
External Email - Use Caution
Hello Freesurfer Experts, I have been trying to run mri_cvs_register to bring sub-millimeter data into MNI space, however the final outputs have large deformations to the brain. I have tried with both 0.5 mm and 0.7 mm using their respective sub-milimeter recons. It seems that the issue arises during Step 3(i) as the el_reg_tocvs_avg35_inMNI152.mgz does not have the deformations, but the step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz file does. Does anyone have any guidance on how I can troubleshoot this?
I have attached the recon-all.log file for the 0.7 mm data. If you need me to share any other files, let me know.
FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS
Thank you, Noriana Jakopin
External Email - Use Caution
Hi Lilla, I've attached the log file and the summary log file for mri_cvs_register on the 0.7mm. Yes, the recon for the data was successful.
Thank you! Noriana
On Thu, Sep 3, 2020 at 1:45 PM Noriana Jakopin nejakopin1@gmail.com wrote:
Hello Freesurfer Experts, I have been trying to run mri_cvs_register to bring sub-millimeter data into MNI space, however the final outputs have large deformations to the brain. I have tried with both 0.5 mm and 0.7 mm using their respective sub-milimeter recons. It seems that the issue arises during Step 3(i) as the el_reg_tocvs_avg35_inMNI152.mgz does not have the deformations, but the step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz file does. Does anyone have any guidance on how I can troubleshoot this?
I have attached the recon-all.log file for the 0.7 mm data. If you need me to share any other files, let me know.
FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS
Thank you, Noriana Jakopin
freesurfer@nmr.mgh.harvard.edu
-
Noriana Jakopin -
Zollei, Lilla,Ph.D.