The problem is with the estimate of the FWHM for that run. Can you re-run mri_glmfit and send me the command line and terminal output?
On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
Dear FS experts,
I ran into an error with one of my mri_glmfit-sim executionand was not sure what was going on. The same simulation is currently running for the left hemisphere without any hiccups but I get this following error for the right hemisphere:
cd /home/adits123/Desktop/projectoutputdata /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu May 5 13:16:51 CDT 2016 Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux adits123 setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh
DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = -nan nSimPerJob = 10000 1/1 Thu May 5 13:16:51 CDT 2016 mri_glmfit --y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim mc-z 10000 1.3 /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 --sim-sign pos --fwhm -nan --fsgd /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods --surf fsaverage rh white simbase /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory. Thu May 5 13:16:51 CDT 2016 ERROR: cannot find any csd files
I am not sure what the fwhm is NaN error is and also why it is only showing up for one hemisphere. Any help is appreciated.
Thanks Koushik Govindarajan
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