This is the command line output for mri_glmfit:
------------------------------------------------------------------------------------------------------------------------
[adits123@localhost projectoutputdata]$ mri_glmfit --glmdir
rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd
paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh
gdfReadHeader: reading paireddifftp1tp2.txt
INFO: gd2mtx_method is dods
Reading source surface
/home/adits123/Desktop/projectoutputdata/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/adits123/Desktop/projectoutputdata
cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
contrastpaired.mtx --surf fsaverage rh
sysname Linux
hostname localhost.localdomain
machine x86_64
user adits123
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
logyflag 0
usedti 0
FSGD paireddifftp1tp2.txt
labelmask
/home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.paired-diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.paired-diff.glmdir
Loading y from
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
INFO: gd2mtx_method is dods
Saving design matrix to rh.paired-diff.glmdir/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 149926 points in label.
Pruning voxels by thr: 0.000000
Found 65950 voxels in mask
Saving mask to rh.paired-diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 32101.581527
DOF = 364
Starting fit and test
Fit completed in 0.03265 minutes
Computing spatial AR1 on surface
Residual: ar1mn=inf, ar1std=-nan, gstd=-nan, fwhm=-nan
Writing results
contrastpaired
maxvox sig=4.51832 F=17.8453 at index 50390 0 0 seed=1463164810
mri_glmfit done
---------------------------------------------------------------------------------------------------------------------------
This is mri_glmfit-sim:
---------------------------------------------------------------------------------------------------------------------------
[adits123@localhost projectoutputdata]$ mri_glmfit-sim --glmdir
$SUBJECTS_DIR/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3
--sim-sign pos --cwpvalthresh 0.05
cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
contrastpaired.mtx --surf fsaverage rh
SURFACE: fsaverage rh
log file is
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mc-z.pos.1.3.mri_glmfit-sim.log
cd /home/adits123/Desktop/projectoutputdata
/usr/local/freesurfer/bin/mri_glmfit-sim
--glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim
mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Mon May 9 09:11:28 CDT 2016
Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST
2012 x86_64 x86_64 x86_64 GNU/Linux
adits123
setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
contrastpaired.mtx --surf fsaverage rh
DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = -nan
nSimPerJob = 10000
1/1 Mon May 9 09:11:28 CDT 2016
mri_glmfit --y
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-11863/contrastpaired.mtx
--mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh
--sim mc-z 10000 1.3
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
--sim-sign pos --fwhm -nan --fsgd
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods
--surf fsaverage rh white
simbase
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
FWHM = -nan
ERROR: input FWHM is NaN (not a number).
Check the mask in the glm directory.
Mon May 9 09:11:28 CDT 2016
ERROR: cannot find any csd files
---------------------------------------------------------------------------------------------------------------------
Many thanks for helping me with this Doug.
Regards
Koushik
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 06, 2016 3:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error
something is going wrong because the FWHM is not-a-number (nan). Can you
send the actual terminal output and not just the log file?
On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:
> Thanks for the reply Doug. This is content of my mri_glmfit.log:
>
> ---------------------------------------------------------------------------------------------------
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /home/adits123/Desktop/projectoutputdata
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
> contrastpaired.mtx --surf fsaverage rh
> sysname Linux
> hostname localhost.localdomain
> machine x86_64
> user adits123
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
> logyflag 0
> usedti 0
> FSGD paireddifftp1tp2.txt
> labelmask
> /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
> maskinv 0
> glmdir rh.paired-diff.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> ResidualFWHM -nan
> SearchSpace 32101.581527
> anattype surface
> ---------------------------------------------------------------------------------------------------------
>
> The left hemisphere says pretty much the same thing, with the ResidualFWHM
> 0.000000 and SearchSpace 44094.721767
>
> Thanks
> Koushik
>
> _______________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, May 06, 2016 10:46 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_glmfit-sim error
>
> The problem is with the estimate of the FWHM for that run. Can you
> re-run mri_glmfit and send me the command line and terminal output?
>
> On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
>> Dear FS experts,
>>
>> I ran into an error with one of my mri_glmfit-sim execution
>> and was not sure what was going on. The same simulation is currently
>> running for the left hemisphere without any hiccups but I get this
>> following error for the right hemisphere:
>> -----------------------------------------------------------------------------------------------------------------------
>> cd /home/adits123/Desktop/projectoutputdata
>> /usr/local/freesurfer/bin/mri_glmfit-sim
>> --glmdir
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim
>> mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>>
>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>> Thu May 5 13:16:51 CDT 2016
>> Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6
>> 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>> adits123
>> setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
>> FREESURFER_HOME /usr/local/freesurfer
>>
>> Original mri_glmfit command line:
>> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
>> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
>> contrastpaired.mtx --surf fsaverage rh
>>
>> DoSim = 1
>> UseCache = 0
>> DoPoll = 0
>> DoPBSubmit = 0
>> DoBackground = 0
>> DiagCluster = 0
>> gd2mtx = dods
>> fwhm = -nan
>> nSimPerJob = 10000
>> 1/1 Thu May 5 13:16:51 CDT 2016
>> mri_glmfit --y
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
>> --C
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx
>> --mask
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim
>> mc-z 10000 1.3
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>> --sim-sign pos --fwhm -nan --fsgd
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd
>> dods --surf fsaverage rh white
>> simbase
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>> FWHM = -nan
>> ERROR: input FWHM is NaN (not a number).
>> Check the mask in the glm directory.
>> Thu May 5 13:16:51 CDT 2016
>> ERROR: cannot find any csd files
>> --------------------------------------------------------------------------------------------------------------------------------
>>
>> I am not sure what the fwhm is NaN error is and also why it is only
>> showing up for one hemisphere. Any help is appreciated.
>>
>> Thanks
>> Koushik Govindarajan
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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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
>
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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
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