Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again just autorecon2 and autorecon3 Best, Paul
On Fri, May 19, 2017 at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
it depends on how many connections there are
On Fri, 19 May 2017, miracle ozzoude wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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