Hi Graham,
I think the distance error is in the creation of the ?h.qsphere.nofix and can be ignored as can the others. It shouldn't be reported and I'll try to find the time to take it out as there is no metric perservation in the qsphere - it's only concerned with topology.
cheers Bruce
On Mon, 3 Jun 2013, Graham Wideman wrote:
Hi all,
I'm testing recon-all using bert with the intent of ensuring that freesurfer installation is good.
recon-all completes with a "finished without error" message, and the resulting surfaces and parcellations look sensible. However, a couple of types of errors are showing up in the log whose significance I'd like to understand.
I have attached the recon-all log, and there are snippets below. The two types of error are:
- mri_em_register: LINE SEARCH FAILED
I see that this has been reported to the list about a dozen times, and the reply usually is that this message is seen occasionally for unknown reasons, but it's not a concern. For me it pops up consistently for the bert sample data, multiple times per run.
In case someone wants to investigate, or interpret the error message, I found docs here: http://www.dtcenter.org/com-GSI/users/docs/codeHTML/comGSIv2browser/html_co de/subroutine/qnewton.f90.html
According to those docs, "INFO=3" means the function is complaining that it didn't converge within a specified number of iterations. Which doesn't sound desirable.
- mris_sphere: distance error %100000.0
An error of 100,000% sounds like a problem. :-(
I'd appreciate hearing what the thinking is on these problems.
Thanks,
-- Graham
Subject bert2 recon-all.log
[Line 630 invoke] mri_em_register -skull nu.mgz /aaa_bin/freesurfer53c6/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ... [Line 746 error] 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: 009: -log(p) = -0.0 tol 0.000010 [Similar errors also at: ] 778, 1010, 1042, 2328, 2360
=========================== [Line 3135 invoke] mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix ... [Line 3232 error] distance error %100000.00 [Similar error at:] 4927 ===========================
#------------------------------------------
Started at Wed May 29 03:18:17 PDT 2013 Ended at Wed May 29 09:18:38 PDT 2013 #@#%# recon-all-run-time-hours 6.006 recon-all -s bert2 finished without error at Wed May 29 09:18:38 PDT 2013