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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
On 07/02/2018 01:48 AM, Soan Duong wrote:
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.
This turns off the routine which tries to figure out whether the registration failed or not. It is ok to turn it off, but you should check whether the registration actually failed or not.
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.
What did you use as input from the MP2RAGE? You cannot use the T1 image, that will surely fail.
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
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Soan Duong