Re: [Freesurfer] Data sets with enlarged ventricles

Hi Khoi

I would recommend trying out version 6 and using the bigventricles flag. It works pretty well

cheers Bruce On Thu, 26 Jul 2018, Khoi Mai wrote:

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Hello, We are trying to run two subjects through recon-all. The kicker is that these two have very large ventricles and we have been stuck at mris_fix_topology (the script reports about 100-ish defects for each). We use HPC to run the analyses but even with a walltime of 96 hours each, both subjects were unable to be finished within that time frame. My question is that is there any way to improve mris_fix_topology runtime?

Subject 1: [IMAGE]

Subject 2:  [IMAGE]

Thank you for your help.

Best,

Khoi