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>>
> 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
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mask.nii.gz
Description: GNU Zip compressed data
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