Hi Angela, Use mris_euler_number on the pial surface, but the probability that there will be any defect is indeed relatively low. Have you carefully checked your white and pial surface slice by slice overlaid on the T1? Sometimes a small region where the surfaces are "wrinkled" is responsible for this error. If this is the case, edit the wm and rerun autorecon2-wm and autorecon3. If this is not the case, i.e. if you don't see anything to edit in the wm, then the best solution is to rerun autorecon2-wm and autorecon3 with the randomness flag. That should solve the issue.
As for your second question, if this is the same subject than the one you got the error, the solution above should solve it. If not, I would advise reprocessing it. Hope it helps, Marie On Aug 3, 2014, at 9:28 AM, <angela.fav...@unipd.it> wrote: > Hi all, > I am running lgi analyses in 5.3 FS version (lion OSX) > > one of my subjects failed with a typical message: > > lGI for vertex number 39901 of the outer mesh is 1.8067 > ... remeasuring lGI value for vertex iV = 40001. It may take a few minutes. > WARNING -- Problem for vertex iV = 40001, lGI value is aberrantly high > (lGI=42.8793)... > ...lGI computation will be stopped. This may be caused by topological > defects, check mris_euler_number on the pial surface. > > Before running again the command mris_compute_lgi I want to check for the > presence of topological defects > > I have some questions: > 1. which is the command line for the command mris_euler_number or - better > - which are the surface files to control for? (lh.orig, lh.pial, lh.white, > etc...) > > 2. I have performed the command check_subject and in all my subjects > appear this message: > > [host-001:~/Desktop/risonanze/studyfree] angelafavaro% check_subject subj061 > CHECKING SUBJECT subj061 > WARN: time for rh.white is older than rh.inflated > WARN: lh.rh.sphere.reg is empty/missing > WARN: time for lh.white is older than lh.inflated > > What is the problem (if any)? > > Thank you for any help > > Angela > > > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
