Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote: > Hi Doug, > It seems ok, no isolated voxels. > I attach it. > Any other ideas? > Thanks, > Eiran > > > > On Friday, March 6, 2015 6:22 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > > > > 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> > > <mailto: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> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto: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 <mailto: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/ > > > > 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. > > >
-- 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
