Hi Meng

we can't diagnose either of these issues without more information and possibly some screen shots. The topology fixer will take a very long time if the initial surfaces have large defects. You can view these by visualizing the ?h.inflated.nofix and ?h.orig.nofix.

The -openmp flag works for us. Are you sure that you have mutliple threads available?

cheers Bruce

On Thu, 14 Sep 2017, Meng Li wrote:

Hi all,

I tried to use FreeSurfer version 6.0.0 to process fifteen subjects, but half of the subjects was stuck at the ‘Correcting Defect’ step. However, when I changed to FreeSurfer version 5.3.0, the ‘Correcting defect’ step finished successfully. Is it possibility that the unsuccessful ‘Correcting Defect’ step is caused by the different versions of Freesurefer?

In addition, when I added the flag -parallel -openmp 30 based on the version 6.0.0, the recon-all –all runtime still need 20+ hours. It seems that the parallel processing did not reduce the processing time. I wonder why the parallel processing did’t save time?

Any help would be greatly appreciated.

Meng