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> 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/
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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.
