Thanks for the reply Doug. This is content of my mri_glmfit.log: --------------------------------------------------------------------------------------------------- $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/adits123/Desktop/projectoutputdata cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh sysname Linux hostname localhost.localdomain machine x86_64 user adits123 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paireddifftp1tp2.txt labelmask /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.paired-diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 ResidualFWHM -nan SearchSpace 32101.581527 anattype surface ---------------------------------------------------------------------------------------------------------
The left hemisphere says pretty much the same thing, with the ResidualFWHM 0.000000 and SearchSpace 44094.721767 Thanks Koushik _______________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, May 06, 2016 10:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error 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 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: > ----------------------------------------------------------------------------------------------------------------------- > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=BQIBAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=BggIQggY76Oebm525cL3bUb9izcgjTD6_4vfkjef8D8&s=3c7uri11bRrp6EP-VQMGPCg9-aReCCqRqnleGrzIu60&e= -- Douglas N. 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