---------- Forwarded message ----------
From: miracle ozzoude <miracoo...@gmail.com>
Date: Fri, Jan 26, 2018 at 7:08 PM
Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hello Doug,
Thanks for the patience. Here's the output from the terminal when I ran
mri_glmfit.
Best,
Paul
/Applications/freesurfer
START: LONGITUDINAL CORTICAL THICKNESS
1000
1000_1
1000_1.long.1000
1000_2
1000_2.long.1000
1001
1001_1
1001_1.long.1001
1001_2
1001_2.long.1001
1003
1003_1
1003_1.long.1003
1003_2
1003_2.long.1003
1005
1005_1
1005_1.long.1005
1005_2
1005_2.long.1005
1008
1008_1
1008_1.long.1008
1008_2
1008_2.long.1008
1013
1013_1
1013_1.long.1013
1013_2
1013_2.long.1013
1014
1014_1
1014_1.long.1014
1014_2
1014_2.long.1014
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX 76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/
ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/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 /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh --cortex
--glmdir lh.paired.diff.glmdir
sysname Darwin
hostname opennet-33-172.uhnres.utoronto.ca
machine x86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
logyflag 0
usedti 0
FSGD paired_diff.fsgd
labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.paired.diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired.diff.glmdir
Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to lh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149955 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to lh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 8.33333e-05 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0 F=0 at index 0 0 0 seed=1517221145
age
maxvox sig=0 F=0 at index 0 0 0 seed=1517221145
mri_glmfit done
gdfReadHeader: reading paired_diff.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 76 3.70328
Class Means of each Continuous Variable
1 ADEX 76.0000
INFO: gd2mtx_method is doss
Reading source surface /Users/carm/Documents/Cas/
ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/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 /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018
cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh --cortex
--glmdir rh.paired.diff.glmdir
sysname Darwin
hostname opennet-33-172.uhnres.utoronto.ca
machine x86_64
user carm
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
logyflag 0
usedti 0
FSGD paired_diff.fsgd
labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/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 /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to rh.paired.diff.glmdir/Xg.dat
Normalized matrix condition is 1686.7
Matrix condition is 2.46289e+06
Found 149926 points in label.
Pruning voxels by thr: 0.000000
Found 0 voxels in mask
Saving mask to rh.paired.diff.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 0.000000
DOF = 5
Starting fit and test
Fit completed in 0.0001 minutes
Computing spatial AR1 on surface
WARNING: ar1 = nan <= 0. Setting fwhm to 0.
Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000
Writing results
mean
maxvox sig=0 F=0 at index 0 0 0 seed=1517884366
age
maxvox sig=0 F=0 at index 0 0 0 seed=1517884366
mri_glmfit done
On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> can you send the terminal output of mri_glmfit?
>
>
> On 01/24/2018 02:52 PM, miracle ozzoude wrote:
> > Hello Doug,
> >
> > I looked at the fwhm.dat and fwhm value = 0. I have attached the
> > mri_glmfit.log file. How do i solve this problem?
> >
> > Best,
> > Paul
> >
> > On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > If your fwhm is 0, then something is wrong. Look in the fwhm.dat
> > file in
> > the glmfit output to see what the value is. Also, send the terminal
> > output from mri_glmfit (not mri_glmfit-sim)
> >
> >
> > On 01/22/2018 11:43 AM, miracle ozzoude wrote:
> > >
> > > ---------- Forwarded message ----------
> > > From: *miracle ozzoude* <miracoo...@gmail.com <mailto:
> miracoo...@gmail.com>
> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>
> > > Date: Sat, Jan 20, 2018 at 1:56 PM
> > > Subject: Re: [Freesurfer] monte-carlo error in longitudinal
> pipeline
> > > 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>>>
> > >
> > >
> > > Hello Doug,
> > >
> > > I tried using the MC tables that FS distributed. However, i got an
> > > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked
> and
> > > there's no fwhm00, the table starts from fwhm01 to fwhm30. Below
> are
> > > my script and cache.mri_glmfi-sim.log files. My FreeSurfer
> > version is
> > > stable version 5.3 on mac. Thank you.
> > >
> > > Best,
> > > Paul
> > >
> > > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
> > > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache
> > 3 pos
> > > --cwpvalthresh 0.05 --2spaces --overwrite
> > > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
> > > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache
> > 3 pos
> > > --cwpvalthresh 0.05 --2spaces --overwrite
> > >
> > > On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
> > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > Why are you doing your own MC simulation? You can just use the
> > > tables that we distribute ...
> > >
> > >
> > > On 1/17/18 6:12 PM, miracle ozzoude wrote:
> > >> Hello Experts,
> > >>
> > >> I am running a paired t-test cortical thickness analysis
> > based on
> > >> the instruction on the wiki page
> > >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>
> > >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>>).
> > >> However, the monte carlo files weren't not created when i
> > >> corrected for multiple comparisons. Below are my script, fsgd
> > >> files, mc-z log file, and a screenshot of contrast folder
> > missing
> > >> mc.z maps. Please can you help me figure out why the error is
> > >> happening. Thank you.
> > >>
> > >> Best,
> > >> Paul
> > >>
> > >> *Script*:
> > >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
> > >> martrix2=age.mtx
> > >> #resample each subjects's left and right hemisphere data to
> > >> fsavarage.
> > >> mris_preproc --target fsaverage --hemi lh --meas thickness
> > --out
> > >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> > >> mris_preproc --target fsaverage --hemi rh --meas thickness
> > --out
> > >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> > >> # #smoothen the concatenated file by 5mm FWHM. --cortex means
> > >> only smooth areas in the cortex. N:B. FWHM changes based on
> > study
> > >> type.
> > >> mri_surf2surf --hemi lh --s fsaverage --sval
> > >> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
> > >> lh.paired-diff.thickness.sm05.mgh
> > >> mri_surf2surf --hemi rh --s fsaverage --sval
> > >> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
> > >> rh.paired-diff.thickness.sm05.mgh
> > >> # #Run GLM analysis
> > >> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd
> $paired
> > >> --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex
> > --glmdir
> > >> lh.paired-diff.glmdirir
> > >> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd
> $paired
> > >> --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex
> > --glmdir
> > >> rh.paired-diff.glmdir
> > >> # # #Run Clusterwise correction for multiple comparisons using
> > >> MONTE CARLO. First create a table for of simulations
> > >> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z
> > 10000 2
> > >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces
> > --overwrite
> > >> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z
> > 10000 2
> > >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces
> > --overwrite
> > >> *Fsgd file 1:pairs.fsgd*
> > >>
> > >> GroupDescriptorFile 1
> > >>
> > >> Class ADEX
> > >>
> > >> Input 1000_1 ADEX
> > >>
> > >> Input 1000_2 ADEX
> > >>
> > >> Input 1001_1 ADEX
> > >>
> > >> Input 1001_2 ADEX
> > >>
> > >> Input 1003_1 ADEX
> > >>
> > >> Input 1003_2 ADEX
> > >>
> > >> Input 1005_1 ADEX
> > >>
> > >> Input 1005_2 ADEX
> > >>
> > >> Input 1008_1 ADEX
> > >>
> > >> Input 1008_2 ADEX
> > >>
> > >> Input 1013_1 ADEX
> > >>
> > >> Input 1013_2 ADEX
> > >>
> > >> Input 1014_1 ADEX
> > >>
> > >> Input 1014_2 ADEX
> > >>
> > >> *Fsgd file 2: paired_diff.fsgd*
> > >>
> > >> GroupDescriptorFile 1
> > >>
> > >> Class ADEX
> > >>
> > >> Variables Age
> > >>
> > >> Input 1000 ADEX 72
> > >>
> > >> Input 1001 ADEX 76
> > >>
> > >> Input 1003 ADEX 72
> > >>
> > >> Input 1005 ADEX 80
> > >>
> > >> Input 1008 ADEX 72
> > >>
> > >> Input 1013 ADEX 80
> > >>
> > >> Input 1014 ADEX 80
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > >
> > > _______________________________________________
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu
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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
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> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har
> vard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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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>
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