Hi Louis

I manage to replicate the error by using wm-anat-snr directly on bert in /usr/local/freesurfer/subjects. I think think the error is in wm-anat-snr and it interactions with mri_segstats.

mri_segstats -all-info ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/10/15-19:39:47-GMT BuildTimeStamp: Jun 20 2012 12:45:04 CVS: $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ User: knutjb Machine: dmed5549 Platform: Linux PlatformVersion: 3.5.0-17-generic CompilerName: GCC CompilerVersion: 40100

Knut J

On 10/15/2012 04:50 PM, Louis Nicholas Vinke wrote:

Hi Knut, It should run by default. Did you check the summary log file, $SUBJECTS_DIR/QA/recon_checker.ALL.summary.log? Otherwise, could you send the terminal output when you run QAtools on a single subject? -Louis

On Sun, 14 Oct 2012, Knut J Bjuland wrote:

...

Hi,

I have downloaded the latest QA_tools v1.1 from http://surfer.nmr.mgh.harvard.edu/fswiki/QATools. However, when I ran

recon_checker, I did not get a signal to noise calculations. I ran recon_checker with -s-dir subjectfile and -snaps-detailed. Is there any option that I missed? Is it possible to download a newer version from cvs?

Knut J

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