Hi Angela
1. if recon-all has completed successfully there shouldn't be any topological defects. You can run mris_euler_number on lh.pial and rh.pial. The Euler number for a closed surface with no defects should be 2.
2. This means something has been rerun but not to completion. You should be able to run
recon-all -s <subject> -sd <subjects_dir> -make all
and it will rerun whatever it needs to
cheers Bruce
On Sun, 3 Aug 2014, angela.favaro@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:
- 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...)
- 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
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