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

 

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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