I ran into an error with one of my mri_glmfit-sim execution and 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:
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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
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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.