Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of recon-all stage from autorecon2. Best, Paul
On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm
On Fri, 19 May 2017, miracle ozzoude wrote:
Hello Bruce, Yes, the skull is still attached. Should I remove the skull
for all the slices and re-run it again? Best, Paul
On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Paul
you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul
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