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
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