Hi Doug,
I am attaching the permutation log file.
Thanks!
Pablo
Date: Mon, 17 Aug 2015 11:15:14 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: Permutation output
Can you send me the log file from the glmdir folder? The log file
that has "perm" in the name?
On 8/12/15 11:33 AM, pablo najt wrote:
Will do that from now on. the output is as follow:
This is the output I am getting which I believe is not what
I need for check the permutation output
C.dat F.mgh cnr.mgh gamma.mgh gammavar.mgh maxvox.dat sig.mgh
> Date: Wed, 12 Aug 2015 11:17:38 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FW: Permutation output
>
> look in the folder of one of the contrasts (eg,
> rh-Diff-BD-HC-Intercept-sulc). Also, if you can paste
such text into the
> email it is much more convenient for us than to sent us
a tiff
>
> On 08/12/2015 11:12 AM, pablo najt wrote:
> > Dear FS exp,
> > In case my message got swamped, I am reposting my
question.
> > Many thanks!
> > Pablo
> >
> >
------------------------------------------------------------------------
> > From: pablon...@hotmail.com
> > To: freesurfer@nmr.mgh.harvard.edu
> > Date: Tue, 11 Aug 2015 11:02:54 +0000
> > Subject: Re: [Freesurfer] Permutation output
> >
> > Thanks. Sorry but I am not being able to figure it
out yet. Basically
> > I am not getting the expected outcome.
> > So I thought to give you an idea of how I am
running permutations.
> >
> > mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm
5000 1.3 perm.neg.13
> > --sim-sign neg
> >
> > And I am attaching a snapshot of the output files
and the log of
> > mdi_glmfit-sim.
> > At this stage I am wondering whether in order to
run permutation it is
> > required use as input the output from fsgd rather
than qdec, because
> > my input is from qdec. Would this make any
difference?
> > Thanks.
> > Pablo
> >
> > > Date: Mon, 10 Aug 2015 11:13:13 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Permutation output
> > >
> > > It is the same thing, but the permutation
output will have the name you
> > > gave the csdbase when you ran the simulation
(ie, the 4th arg to --sim)
> > >
> > > On 08/10/2015 05:54 AM, pablo najt wrote:
> > > > Thank you Doug.
> > > > I run permutations with mdi_glmfit-sim
--sim perm. Would you be able
> > > > to advice on the output and how to open
the permutation outputs? The
> > > > tutorial instructs on how to open the
*.summary file for the summary
> > > > of clusters and *.sig.cluster.mgh the
cluster corrected map, but not
> > > > the permutation output.
> > > > Thank you,
> > > > Pablo
> > > >
> > > >
> >
------------------------------------------------------------------------
> > > > Date: Fri, 7 Aug 2015 10:53:55 -0400
> > > > From: gr...@nmr.mgh.harvard.edu
> > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > Subject: Re: [Freesurfer] Correction for
multiple comparisons - qdec
> > > >
> > > > You can try permutation, though it is
often more constraining than
> > > > those other two options. To do this,
you'll need to run
> > mri_glmfit-sim
> > > > from the command line using the --sim
perm option. Run it with --help
> > > > to get examples
> > > >
> > > > On 8/7/15 6:59 AM, pablo najt wrote:
> > > >
> > > > Dear FS experts,
> > > > I have a question about running
corrections for multiple
> > > > comparisons. I am finding a fairly large
cluster analyzing 2
> > > > groups on sulcal depth. However when I
tried FDR or cluster wise
> > > > correction the results do not seem to
survive. As the result is on
> > > > the region I was predicting I want to
make sure there are no other
> > > > options for correcting for multiple
comparisons. I am including a
> > > > figure of my result to give you an idea
of the size of the
> > > > cluster. Do you have any suggestions for
trying alternative ways
> > > > of correcting?
> > > > Thank you in advance,
> > > > Pablo
> > > >
> > > >
> > > >
> > > >
_______________________________________________
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> > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > >
> > > >
> > > >
_______________________________________________ Freesurfer
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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:
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> > >
> > >
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> >
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> >
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The
> > information in this e-mail is intended only for
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> > the e-mail contains patient information, please
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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/
>
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_______________________________________________
Freesurfer mailing list
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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
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
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cd /Volumes/NEW_VOLUME/GBS/glmdir
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Sun 9 Aug 2015 12:25:48 IST
Darwin .imac.nuigalway.ie 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18
16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64
setenv SUBJECTS_DIR /Volumes//NEW_VOLUME/GBS
FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit --y /Volumes/NEW_VOLUME/GBS/qdec/rh_sulc_fwhm25/y.mgh --fsgd
/Volumes/NEW_VOLUME/GBS/qdec/rh_sulc_fwhm25/qdec.fsgd dods --glmdir
/Volumes/NEW_VOLUME/GBS/qdec/rh_sulc_fwhm25 --surf fsaverage rh --label
/Volumes/NEW_VOLUME/GBS/fsaverage/label/rh.aparc.label --C
/Volumes/NEW_VOLUME/GBS/qdec/rh_sulc_fwhm25/contrasts/rh-Avg-Intercept-sulc.mat
--C
/Volumes/NEW_VOLUME/GBS/qdec/rh_sulc_fwhm25/contrasts/rh-Diff-BD-HC-Intercept-sulc.mat
DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 0
nSimPerJob = 5000
1/1 Sun 9 Aug 2015 12:25:48 IST
mri_glmfit --y rh_sulc_fwhm25/y.mgh --C
rh_sulc_fwhm25/tmp.mri_glmfit-sim-10121/rh-Avg-Intercept-sulc.mtx --C
rh_sulc_fwhm25/tmp.mri_glmfit-sim-10121/rh-Diff-BD-HC-Intercept-sulc.mtx --mask
rh_sulc_fwhm25/mask.mgh --sim perm 5000 1.3 rh_sulc_fwhm25/csd/perm.neg.13.j001
--sim-sign neg --fwhm 0 --fsgd rh_sulc_fwhm25/y.fsgd dods --label
/Volumes/NEW_VOLUME/GBS/fsaverage/label/rh.aparc.label --surf fsaverage rh white
simbase rh_sulc_fwhm25/csd/perm.neg.13.j001
FWHM = 0.000000
gdfReadHeader: reading rh_sulc_fwhm25/y.fsgd
INFO: gd2mtx_method is dods
Reading source surface /Volumes//NEW_VOLUME/GBS/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 /Volumes/NEW_VOLUME/GBS/glmdir
cmdline mri_glmfit --y rh_sulc_fwhm25/y.mgh --C
rh_sulc_fwhm25/tmp.mri_glmfit-sim-10121/rh-Avg-Intercept-sulc.mtx --C
rh_sulc_fwhm25/tmp.mri_glmfit-sim-10121/rh-Diff-BD-HC-Intercept-sulc.mtx --mask
rh_sulc_fwhm25/mask.mgh --sim perm 5000 1.3 rh_sulc_fwhm25/csd/perm.neg.13.j001
--sim-sign neg --fwhm 0 --fsgd rh_sulc_fwhm25/y.fsgd dods --label
/Volumes/NEW_VOLUME/GBS/fsaverage/label/rh.aparc.label --surf fsaverage rh
white
sysname Darwin
hostname .imac.nuigalway.ie
machine x86_64
user
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Volumes/NEW_VOLUME/GBS/glmdir/rh_sulc_fwhm25/y.mgh
logyflag 0
usedti 0
FSGD rh_sulc_fwhm25/y.fsgd
labelmask /Volumes/NEW_VOLUME/GBS/fsaverage/label/rh.aparc.label
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from /Volumes/NEW_VOLUME/GBS/glmdir/rh_sulc_fwhm25/y.mgh
_______________________________________________
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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
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