External Email - Use Caution
Dear FreeSurfer,
My name is Soan Duong. I used FreeSurfer to segmentation some high-resolution T1w images (resolution of 0.5x0.533x0.533, size of 288x378x420), and got a couple of problems:
1. I ran the command: recon-all -i DH_anat.nii -s DH -all, then got stuck with the error of Talairach failed!. I searched on the Internet and a guy suggested adding -notal-check flag in the command.
I was successful with running recon-all -i DH_anat.nii -s DH -all -notal-check, but not understand about the added flag.
2. I ran recon-all with 3 T1w images of 3 subjects (with the same MP2RAGE sequence), the segmentation of a subject is weird (please see the image axial_245.png in the attachment). It seems to me that the left and right separation is not correct. Please noted that the other two segmentation is fine. I have attached the recon-all log files of the image with problem.
3. The segmentation results are down-resolution. Thus I tried to run recon-all with -hires flag: recon-all -i DH_anat.nii -s DH -all -hires -expert expert.opts -notal-check.
The recon-all has been getting stuck with 'CORRECTING DEFECT 43 (vertices=65073, convex hull=7583, v0=36813' on the terminal screen for nearly one week. I have attached the used expert file.
I am having trouble figuring out where these issues are coming from and how to solve them. I was wondering if you would have any ideas on what might going wrong/how to address it? Any help you have to offer would be greatly appreciated.
Best regards, Soan
--- Soan Duong PhD Candidate School of Electrical, Computer and Telecommunications Engineering Faculty of Engineering and Information Sciences University of Wollongong Northfields Avenue, Wollongong, NSW 2522, Australia
