For some reason the spatial fwhm calculation is failing. This sometimes happens if the mask is highly fractured. Can you look at group.glm/mask.nii.gz and see if there are a bunch of isolated voxels?
On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote: > > > > > Hi Doug, > Thanks for your reply. > This is the terminal output: > > [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz --surface fsaverage lh > Reading source surface > /Applications/freesurfer/subjects/fsaverage/surf/lh.white > Number of vertices 163842 > Number of faces 327680 > Total area 65416.648438 > AvgVtxArea 0.399267 > AvgVtxDist 0.721953 > StdVtxDist 0.195470 > > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > cwd > /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr > cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz --surface fsaverage lh > sysname Darwin > hostname Eran-Harels-MacBook-Pro.local > machine i386 > user eiran > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 1 > y > > /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz > logyflag 0 > usedti 0 > labelmask > /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label > maskinv 0 > glmdir group.glm > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > wFile cesvar.nii.gz > weightinv 1 > weightsqrt 1 > Creating output directory group.glm > Loading y from > /Applications/freesurfer/BSMT_PROJECT/doors_group_51014/doors11.lh/r-vs-nr/ces.nii.gz > Saving design matrix to group.glm/Xg.dat > Normalized matrix condition is 1 > Matrix condition is 1 > Found 149955 points in label. > Pruning voxels by thr: 0.000000 > Found 75351 voxels in mask > Saving mask to group.glm/mask.nii.gz > Reshaping mriglm->mask... > search space = 36561.555889 > DOF = 26 > Starting fit and test > Fit completed in 0.0542833 minutes > Computing spatial AR1 on surface > Residual: ar1mn=inf, ar1std=nan, gstd=nan, fwhm=nan > Writing results > osgm > maxvox sig=5.1359 F=31.1425 at index 47512 0 0 seed=1425981217 > mri_glmfit done > > Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% > mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 > cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm > --glmdir group.glm --nii.gz --surface fsaverage lh > SURFACE: fsaverage lh > log file is group.glm/cache.mri_glmfit-sim.log > > cd > /applications/freesurfer/bsmt_project/doors_group_51014/doors11.lh/r-vs-nr > /Applications/freesurfer/bin/mri_glmfit-sim > --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 > > $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ > Wed Mar 4 20:55:33 IST 2015 > Darwin Eran-Harels-MacBook-Pro.local 10.8.0 Darwin Kernel Version > 10.8.0: Tue Jun 7 16:33:36 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_I386 i386 > eiran > setenv SUBJECTS_DIR /Applications/freesurfer/subjects > FREESURFER_HOME /Applications/freesurfer > > Original mri_glmfit command line: > cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > group.glm --nii.gz --surface fsaverage lh > > DoSim = 0 > UseCache = 1 > DoPoll = 0 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = dods > fwhm = nan > ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd > > Any ideas? > Thanks, > Eiran > > Subject: Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638 > Date: Mon, 02 Mar 2015 14:17:39 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > That is strange. Can you send the full terminal output from the first > call to mri_glmfit-sim? > doug > > On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: > > > Hello Freesurfers, > > > > I use freesurfer v5.3.0 > > > > When I do group analysis correction for multiple comparisons for lh as > > follows: > > > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > > group.glm --nii.gz --surface fsaverage lh > > > > mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 > > > > I get this error message: > > > > ERROR: cannot find > > > /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd > > > > For the mkanalysis-sess i used fwhm = 5. > > > > When i do the same for mni305 and use: > > > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir > > group.glm --nii.gz > > > > mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 > > > > It works well without an error. > > > > Thanks, > > Eiran > > > > -- 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.
