Good morning Doug,
Thank you for your help.
I followed your advise and unfortunately I do not understand why after
adding the threshold 2 cwpvalthresh .025 in order to do the correction across
lh and rh I still get in my clusters summary and clusters with cwp>.01 as well
as cwp> .025.
This is what I was running:
mri_glmfit-sim \
--glmdir rh.age.glmdir \
--cache 2 neg \
--cwpvalthresh .025 \
--overwrite
And this is my output:
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
1 -6.24 104279 2004.41 6.4 -83.6 34.4 0.0001 0 0 3539 cuneus
2 -5.71 56656 2923.03 24.4 25.4 37.1 0.0001 0 0 5020 superiorfrontal
3 -4.89 156133 1826.82 5.1 -29.7 38.6 0.0001 0 0 4324 posteriorcingulate
4 -4.57 117278 1917.42 43.2 43.4 -8.2 0.0001 0 0 3393 parsorbitalis
5 -4.32 134603 910.13 10.5 45.7 -9.2 0.0009 0 0 1597 medialorbitofrontal
6 -4.01 47845 1018.06 38.9 -73.9 34.6 0.0003 0 0 1802 inferiorparietal
7 -3.97 12268 580.81 14.2 -51 63.3 0.0132 0.01 0.01 1415 superiorparietal
8 -3.78 54798 871.02 53 -39.7 -5.1 0.0010 0 0 1969 bankssts
9 -3.78 21941 555.51 45.8 -28.2 6.4 0.0175 0.02 0.02 1369 superiortemporal
10 -2.91 86118 884.25 10.1 -98.9 11.7 0.0010 0 0 1089 lateraloccipital
11 -2.86 13271 674.26 21.5 -65.4 -6.1 0.0056 0 0.01 722 lingual
Is this right?
Please advise.
Thank you.
Antonella
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, August 23, 2011 4:33 PM
Subject: Re: [Freesurfer] correction for multiple comparisons
Yes, that is correct, you should use .025 if you are correcting for both
hemispheres.
doug
Antonella Kis wrote:
>
> Hi Doug,
>
> I would like to run the correction for multiple comparisons. I know
> glmfit-sim corrects for multiple comparisons. My question is:
>
> the corrections for multiple comparisons will be done while running
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --overwrite
>
> or I need to add --cwpvalthresh .025 before --overwrite. I found
> on-line that setting a treshold = 2 means p < 0.05 but adding
> --cwpvalthresh .025 will do the correction across 2 spaces: lh and rh:
> .025 = .05/2
> Bonferroni Correction and will show only the clusters with p<.025.
>
> Is this right? So to run for multiple corrections in fact I will need
> to run:
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --cwpvalthresh .025
> --overwrite
>
> Please advise me.
>
> Thank you for your time and help.
> Antonella
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> *To:* Antonella Kis <ator...@yahoo.com>
> *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Monday, August 22, 2011 2:28 PM
> *Subject:* Re: [Freesurfer] GLM or Qdec ?
>
>
>
> Antonella Kis wrote:
> > Dear FS experts,
> >
> > I finished running the GLM and I wonder what is the best way to
> > further analyse my data in order to see if there is any relation
> > between age (at seizure onset) and cortical thickness for my patients
> > versus control group.
> >
> >
> > 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get
> > more clusters than the number of clusters obtained from mri_glmfit-sim?
> When you look at it in tksurfer, you are looking at uncorrected data.
> glmfit-sim corrects for multiple comparisons. Some of the clusters don't
> survive.
> >
> > 2). What sig.mgh represents?
> -log10(p)
> >
> > 3) What's the real significance of a cluster (how a cluster is formed)?
> It is based on the likelihood of getting a cluster of that size by
> chance given the search space (cortical surface area), smoothness
> (FWHM), and cluster-forming threshold (eg, p<.05).
> >
> > 4). Why my thickness value in clusters (eg cluster no. 1 which
> > coresponds to the posteriorcingulate) for subject no.1 is different
> > that the thickness value obtained for the same region in the
> > lh.aparc.stats while running recon-all?
> >
> > 5). After running the GLM should I use visualizing and plotting method
> > to further analyse my data and load FSGD file
> > lh.gender_age.glmdir/y.fsgd?
> >
> > 6). Should my ROI's be defined or be the same with my clusters?
> I don't know what you mean by that.
> >
> > 7). What is the difference between GLM and Qdec? What method is the
> > best to analyse the relation between age and cortical thickness for
> > my patients versus control group?
> They are the same statistically. They are just different ways to provide
> information about your design and contrasts. QDEC is graphical (point
> and click). mri_glmfit you create FSGD files and run it from the
> command-line. QDEC actually creates FSGD files and contrast files and
> runs mri_glmfit.
> >
> > 8). Why when analysing with Qdec I get more clusters? Are this
> > defining or representing the sig.mgh as in GLM?
> They should give identical results when run in the same way. My guess is
> that you have created two different designs and so are getting different
> answers.
> >
> > 9). When using Qdec were I can find as an output of results the
> > number of clusters and the cortical thickness value?
> You'll have to run the correction for multiple comparisons (interface on
> the results page). This simply runs mri_glmfit-sim.
>
> doug
> >
> >
> > Thank you and have a great day!
> > Antonella
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
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> > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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>
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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.
