If you don't care about the affect hemisphere, I think you can just specify to analyze only the unaffected with --hemi lh or --hemi rh
On 1/10/2020 8:19 AM, Horn, Mitchell Jacob wrote: Hi Freesurfer Team,
I have a couple cases with large hemispheric ICH that have caused my recon to hit the default wall-time of 96 hours. It seems to get hung up on the correcting topology defects step for the affected hemisphere. My goal is to have the recon at least finish so I can analyze the unaffected hemisphere.
I have tried WM-edits, and just recently tried generously covering the ICH in the aseg.presurf with the WM-hypointensity label 77. I then submitted the recon to start just after the aseg.presurf generation with the following tags, < recon-all -autorecon2-cp -autorecon3 -subjid $subject >. However, when it gets to the fix topology point for the affected hemisphere, it hangs at this point with a huge defect as shown below:
reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.2324 (-4.6162) -vertex loglikelihood: -6.5360 (-3.2680) -normal dot loglikelihood: -3.5251 (-3.5251) -quad curv loglikelihood: -6.0339 (-3.0169) Total Loglikelihood : -25.3274 CORRECTING DEFECT 0 (vertices=26285, convex hull=5359, v0=0)
Is there something I can do to at least skip the correction of the affected hemisphere?
Thanks in advance,
Mitch
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