Hi,
I'm running recon-all on a cluster using Linux, 64 bit Centos 6. Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.
I first run recon-all -all, then recon-all -localGI
One out of 102 subjects failed the lgi, but the recon-all -all excited without error. During "Computing MAP estimate", however, it did give this error (multiple times):
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA
But I find that in several subjects who also exit recon-all -all without error, so I assume that's OK?
When it exited recon-all -localGI, it produced this warning:
... remeasuring lGI value for vertex iV = 73001. It may take a few minutes. WARNING -- Problem for vertex iV = 73001, lGI value is aberrantly high (lGI=48.6608)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.
ERROR: compute_lgi did not create output file '/usit/abel/u1/rimol/subjects/PD/PD008/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Linux compute-16-31.local 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Although recon-all -all exited without error, should I still be worried, since it appears that there may be topological defects in the pial surface? I've looked at the surfaces and there is one spot that looks suspicious (please see attached screen shot from Freeview).
Thank you!
sincerely yours,
Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway
