Doug,It works well now,Many thanks!,Eiran
On Friday, March 6, 2015 9:28 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu> wrote:
sorry, gave you a linux binary. Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit.mac
On 03/06/2015 02:25 PM, Eiran Vadim Harel wrote:
> Hi Doug,
> It is giving me this error:
> [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
> /Applications/freesurfer/bin/mri_glmfit: line 9: syntax error near
> unexpected token `('
> /Applications/freesurfer/bin/mri_glmfit: line 9: `ELF>
> ?@@(?^@8@,)@@@@@?88@8@@@ꨍꨍ ????????`.?%
> ?ʍ????TT@T@DD??????P?td?????????\?\?Q?t/lib64/ld-linux-x86-64.so.2GNUGNU?L?ьUF?6?'
>
> Thanks,
> Eiran
>
>
> On Friday, March 6, 2015 8:26 PM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu> wrote:
>
>
>
> There appears to be a bug in the computation of the fwhm and it appears
> that I fixed the bug somewhere between 5.3 and now. I've put a new
> version of mri_glmfit here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
>
> see if that works for you
> doug
>
>
> On 03/06/2015 12:38 PM, Douglas N Greve wrote:
> > 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 <mailto: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>>
> >>> <mailto: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>>
> >>> <mailto: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>>
> >> <mailto: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>
> <mailto: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 <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/
>
>
> _______________________________________________
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>
>
>
>
>
> _______________________________________________
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--
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
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_______________________________________________
Freesurfer mailing list
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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.
