Hi Doug,
Since running mri_glmfit-sim will do a correction by multiple comparison (I
suppose is doing a Monte Carlo to remove areas that are not statically
significant) I wonder why I still get clusters with p>0.01? Do I need to apply
FDR before -sim?
Thank you for your time and help.
Antonella
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Cc: Antonella Kis <ator...@yahoo.com>; "freesurfer@nmr.mgh.harvard.edu"
<freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, August 25, 2011 12:23 PM
Subject: Re: [Freesurfer] Fw: fsaverage
That "2" is a voxel-wise threshold used to form the cluster. The cwp is
a cluster-wise threshold used to eliminate non-significant clusters from
the output.
Bruce Fischl wrote:
> I'll leave that for Doug
> On Thu, 25 Aug 2011, Antonella Kis wrote:
>
>> Hi Bruce,
>>
>> Thank you very much for your prompt and helpful answer.
>>
>> I have one more question, please: I do not understand what's the
>> role of adding the threshold value while running the mri_glmfit-sim
>> with --cache
>> since after adding the threshold 2, I still get clusters with
>> cwp>.01.
>> 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?
>>
>> Also, by adding for the lh --cwpvalthresh .025 what exactly means
>> or how the corrections are made for both hemispheres. I know
>> --cwpvalthresh .025
>> shows only clusters p<.025 but then what means cluster significance
>> values not corrected for 2 spaces?
>> 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
>> > >
>> > >
>> > >
>> > >
>> ------------------------------------------------------------------------
>> > >
>> > > _______________________________________________
>> > > Freesurfer mailing list
>> > > 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
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> >
>> > _______________________________________________
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>> > 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
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>> > but does not contain patient information, please contact the sender
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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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>>
>>
>>
>>
>>
>>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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contains patient information, please contact the Partners Compliance HelpLine at
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