[pang@localhost newron-controlDoug]$ mri_glmfit-sim --glmdir rh.rmanova --sim mc-z 5000 4 mc-z.absolute --sim-sign abs --overwrite cmdline mri_glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd fsgd doss --C training-effect.mtx --pca WARNING: unrecognized mri_glmfit cmd option doss /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir rh.rmanova --sim mc-z 5000 4 mc-z.absolute --sim-sign abs --overwrite $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $ Tue Oct 30 15:56:00 EDT 2012 Linux localhost.localdomain 2.6.34.9-69.fc13.x86_64 #1 SMP Tue May 3 09:23:03 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux pang setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = doss fwhm = -nan nSimPerJob = 5000 1/1 Tue Oct 30 15:56:00 EDT 2012 mri_glmfit --y rh.thickness.sm25.mgh --C rh.rmanova/tmp.mri_glmfit-sim-5922/training-effect.mtx --mask rh.rmanova/mask.mgh --sim mc-z 5000 4 rh.rmanova/csd/mc-z.absolute.j001 --sim-sign abs --fwhm -nan --fsgd rh.rmanova/y.fsgd doss INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed simbase rh.rmanova/csd/mc-z.absolute.j001 gdfReadHeader: reading rh.rmanova/y.fsgd INFO: NOT demeaning continous variables Continuous Variable Means (all subjects) 0 TP1-vs-TP2.Group1Trn 0 1 TP1-vs-TP2.Group2Cntrl 0 Class Means of each Continuous Variable 1 Subject1 0.0000 0.0000 2 Subject2 0.0000 0.0000 3 Subject3 0.0000 0.0000 4 Subject4 0.0000 0.0000 5 Subject5 0.0000 0.0000 6 Subject6 0.0000 0.0000 7 Subject7 0.0000 0.0000 8 Subject8 0.0000 0.0000 9 Subject9 0.0000 0.0000 10 Subject10 0.0000 0.0000 11 Subject11 0.0000 0.0000 12 Subject12 0.0000 0.0000 13 Subject13 0.0000 0.0000 14 Subject14 0.0000 0.0000 15 Subject15 0.0000 0.0000 16 Subject16 0.0000 0.0000 17 Subject17 0.0000 0.0000 18 Subject18 0.0000 0.0000 19 Subject19 0.0000 0.0000 20 Subject20 0.0000 0.0000 21 Subject21 0.0000 0.0000 22 Subject22 0.0000 0.0000 23 Subject23 0.0000 0.0000 24 Subject24 0.0000 0.0000 INFO: gd2mtx_method is doss $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /usr/local/freesurfer/subjects/newron-controlDoug cmdline mri_glmfit --y rh.thickness.sm25.mgh --C rh.rmanova/tmp.mri_glmfit-sim-5922/training-effect.mtx --mask rh.rmanova/mask.mgh --sim mc-z 5000 4 rh.rmanova/csd/mc-z.absolute.j001 --sim-sign abs --fwhm -nan --fsgd rh.rmanova/y.fsgd doss sysname Linux hostname localhost.localdomain machine x86_64 user pang FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /usr/local/freesurfer/subjects/newron-controlDoug/rh.thickness.sm25.mgh logyflag 0 usedti 0 FSGD rh.rmanova/y.fsgd mask rh.rmanova/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 DoFFx 0 Loading y from /usr/local/freesurfer/subjects/newron-controlDoug/rh.thickness.sm25.mgh INFO: gd2mtx_method is doss Matrix condition is 1 Found 163842 voxels in mask search space = 163842 DOF = 22 thresh = 4, threshadj = 3.69897 Starting simulation sim over 5000 trials mri_glmfit simulation done Tue Oct 30 16:05:31 EDT 2012 mri_volcluster --in rh.rmanova/training-effect/sig.mgh --csd rh.rmanova/csd/mc-z.absolute.j001-training-effect.csd --mask rh.rmanova/mask.mgh --cwsig rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh --vwsig rh.rmanova/training-effect/mc-z.absolute.sig.voxel.mgh --sum rh.rmanova/training-effect/mc-z.absolute.sig.cluster.summary --ocn rh.rmanova/training-effect/mc-z.absolute.sig.ocn.mgh --csdpdf rh.rmanova/training-effect/mc-z.absolute.pdf.dat NOT Adjusting threshold for 1-tailed test INFO: loading mask volume: rh.rmanova/mask.mgh INFO: MRIbinarize01(): nhits = 163842 Found 163842 voxels in mask Search Space = 163842 mm3 Computing voxel-wise significance CSDpvalMaxSigMap(): found 0/163842 above 0 INFO: Found 60 voxels in threhold range INFO: Found 16 clusters that meet threshold criteria INFO: Found 16 clusters that meet size criteria INFO: Found 16 final clusters INFO: writing summary to rh.rmanova/training-effect/mc-z.absolute.sig.cluster.summary Saving cluster pval rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh INFO: writing OCN to rh.rmanova/training-effect/mc-z.absolute.sig.ocn.mgh mri_volcluster: done mri_convert rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh --frame 0 mri_convert rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) keeping frame 0 writing to rh.rmanova/training-effect/mc-z.absolute.sig.cluster.mgh... Tue Oct 30 15:56:00 EDT 2012 Tue Oct 30 16:05:33 EDT 2012 mri_glmfit-sim done