It looks like over half your voxels have been pruned because they have value identical to 0 in at least one subject
Found 149926 points in label. Pruning voxels by thr: 0.000000 Found 65950 voxels in mask How did you create rh.paired-diff.thickness.sm05.mgh? On 05/09/2016 10:24 AM, Govindarajan, Koushik Athreya wrote: > This is the command line output for mri_glmfit: > > ------------------------------------------------------------------------------------------------------------------------ > [adits123@localhost projectoutputdata]$ mri_glmfit --glmdir > rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd > paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh > gdfReadHeader: reading paireddifftp1tp2.txt > INFO: gd2mtx_method is dods > Reading source surface > /home/adits123/Desktop/projectoutputdata/fsaverage/surf/rh.white > Number of vertices 163842 > Number of faces 327680 > Total area 65020.765625 > AvgVtxArea 0.396850 > AvgVtxDist 0.717994 > StdVtxDist 0.193566 > > $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 > Creating output directory rh.paired-diff.glmdir > Loading y from > /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh > INFO: gd2mtx_method is dods > Saving design matrix to rh.paired-diff.glmdir/Xg.dat > Normalized matrix condition is 1 > Matrix condition is 1 > Found 149926 points in label. > Pruning voxels by thr: 0.000000 > Found 65950 voxels in mask > Saving mask to rh.paired-diff.glmdir/mask.mgh > Reshaping mriglm->mask... > search space = 32101.581527 > DOF = 364 > Starting fit and test > Fit completed in 0.03265 minutes > Computing spatial AR1 on surface > Residual: ar1mn=inf, ar1std=-nan, gstd=-nan, fwhm=-nan > Writing results > contrastpaired > maxvox sig=4.51832 F=17.8453 at index 50390 0 0 seed=1463164810 > mri_glmfit done > > --------------------------------------------------------------------------------------------------------------------------- > > > This is mri_glmfit-sim: > --------------------------------------------------------------------------------------------------------------------------- > [adits123@localhost projectoutputdata]$ mri_glmfit-sim --glmdir > $SUBJECTS_DIR/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 > --sim-sign pos --cwpvalthresh 0.05 > cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y > rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C > contrastpaired.mtx --surf fsaverage rh > SURFACE: fsaverage rh > log file is > /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mc-z.pos.1.3.mri_glmfit-sim.log > > 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 $ > Mon May 9 09:11:28 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 Mon May 9 09:11:28 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-11863/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. > Mon May 9 09:11:28 CDT 2016 > ERROR: cannot find any csd files > > --------------------------------------------------------------------------------------------------------------------- > > Many thanks for helping me with this Doug. > > Regards > 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 3:21 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_glmfit-sim error > > something is going wrong because the FWHM is not-a-number (nan). Can you > send the actual terminal output and not just the log file? > > On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote: >> 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. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=BQIBAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=BggIQggY76Oebm525cL3bUb9izcgjTD6_4vfkjef8D8&s=vX9_ag65D0rP8tJyH0ItQx0FZyBOcmAQ_0pxE-pm5AQ&e= >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=BQIBAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=BggIQggY76Oebm525cL3bUb9izcgjTD6_4vfkjef8D8&s=6Q90ZAC_toVpIf6nQlV3Gz-2pe1eEN_7GbPqtur3Pms&e= >> >> _______________________________________________ >> 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= >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=BQIBAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=BggIQggY76Oebm525cL3bUb9izcgjTD6_4vfkjef8D8&s=Ehy0Ge60dpNd-jdeQnnuoqFvnwLMDgiJdhqihOFTXOY&e= >> . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> _______________________________________________ >> 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=iPzyxLgZjAyu60suqywDg8Xja1nfqgzAH20L2eweRGA&s=kQynqM_ISVG9xm2z2GkuzAksOas5r5-xwBs3xtV_mNo&e= >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: > https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=BQIBAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=iPzyxLgZjAyu60suqywDg8Xja1nfqgzAH20L2eweRGA&s=akkIzopcEC25faTeAeXusXqNfc2_J9DCYizhdsaW7Y0&e= > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=BQIBAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=iPzyxLgZjAyu60suqywDg8Xja1nfqgzAH20L2eweRGA&s=vXYTg5t5ZB1QY8w3Vgfn1Ptp6gcOQwRJRmlsz59QqLE&e= > > _______________________________________________ > 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=iPzyxLgZjAyu60suqywDg8Xja1nfqgzAH20L2eweRGA&s=kQynqM_ISVG9xm2z2GkuzAksOas5r5-xwBs3xtV_mNo&e= > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=BQIBAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU&m=iPzyxLgZjAyu60suqywDg8Xja1nfqgzAH20L2eweRGA&s=EpV645m666Zgd3X3nWh139VMgVz7g_ubLfiiXy_cOgg&e= > . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
