How should I have described the model?
Date: Fri, 30 Jan 2015 13:09:40 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average values per cluster
>>>I told him it the model is a GLM with age, gender and
state as covariates
This is not a sufficient description. Several design matrices could
be derived from this description.
On 1/30/15 11:58 AM, maaike rive wrote:
The p value from SPSS is 0.156. I checked with a
statistician, just to be sure, but he says the SPSS model is
correct... (he doesn't know anything about freesurfer and FSGD
files, but I told him it the model is a GLM with age, gender and
state as covariates).
Date: Fri, 30 Jan 2015 11:46:37 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average values per cluster
You should report the clusterwise p-value. The p-value that
you have computed is not interpretable. If it did not come out
significant, then it would be worrisome, but it is only a
check and cannot be used for anything. What p-value did you
get from SPSS? I'd be curious to know what the source of the
descrpancy is since this has happened several times now.
doug
On 1/30/15 3:25 AM, maaike
rive wrote:
Hi Douglas,
I used the matlab code and the p value is
signifiant, although less so than the p-value I get
from the clusterwise statistics (0.0027 vs 0.00010). (Indeed
I used an abs threshold for the clusterwise statistics).
Which p-value should I report?
Thanks,
Maaike
From: r_maa...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 29 Jan 2015 19:48:44 +0100
Subject: Re: [Freesurfer] average values per cluster
No not yet; I will do so!
> Date: Thu, 29 Jan 2015 13:44:33 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] average values
per cluster
>
>
> The t is correct. When the contrast matrix
only has one row, then the F
> is just an unsigned t. I don't know
anything about SPSS so I can't tell
> from what you have sent whether it is the
same model or not. Try to get
> SPSS to output the design matrix. Did you
try the matlab code below?
>
> On 01/29/2015 01:40 PM, maaike rive wrote:
> > Hi Douglas,
> >
> > I checked but as far as I see it I
used the same models. I attached
> > the SPSS model and output as wel as
the FSGD file and contrast file
> > (to test a diagnosis x age
interaction). Now that I come to think of
> > it, I think the reason for the
discrepant findings is that I used a
> > t-contrast instead of an F-contrast
for the interaction in Freesurfer.
> > Apologies I did not think about this
earlier. But maybe there is
> > something else I did completely wrong.
> >
> > What do you think?
> >
> > If it is indeed the t vs F contrast,
than how should I specify that
> > the contrast is an F-contrast? Is it
ok to just add another line to
> > the contrastfile (so
> > 0 0 0 0 0 0 0 0 1 1 1 1 -1 -1 -1 -1
> > 0 0 0 0 0 0 0 0 -1 -1 -1 -1 1 1 1 1)?
> >
> > Thanks again,
> >
> > Maaike
> >
> > > Date: Mon, 26 Jan 2015 11:23:59
-0500
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] average
values per cluster
> > >
> > >
> > > We get these kind of reports
occasionally. When I ask people to confirm
> > > that they use exactly the same
design matrix in SPSS, I never hear
> > back,
> > > so I assume that it gets
resolved. So please check. The other thing you
> > > can do is to run in matlab,
something like
> > >
> > > cd glmdir/contrast
> > > X = load('Xg.dat');
> > > y = load('ocn.dat');
> > > C = load('C.dat');
> > > [beta rvar] = fast_glmfit(y,X);
> > > [F p] =
fast_fratio(beta,X,rvar,C);
> > > p will be the p-value
> > >
> > > If you used an unsigned
cluster-forming threshold (ie, abs), then it is
> > > possible that some of the voxels
are pos and some are neg so that they
> > > average out
> > >
> > > doug
> > >
> > >
> > >
> > >
> > > On 01/26/2015 09:03 AM, maaike
rive wrote:
> > > > Dear Freesurfer experts,
> > > >
> > > > Sorry to bother you again,
but I have two more questions about
> > > > extracting
(thickness/surface/GI) values from a certain
cluster.
> > > >
> > > > As I understood, the
abs.y.ocn.dat file gives the average values
> > for a
> > > > given significant cluster
(e.g. a cluster where there is a
> > significant
> > > > AxB interaction).
> > > >
> > > > I may be completely
misunderstanding things, but if I use these
> > values
> > > > in SPSS for further
statistics and test the same interaction (AxB),
> > > > than according to SPSS this
interaction is /not /significant
> > > > (corrected for the same
covariates as in the FSGD file).
> > > >
> > > > Could you tell me what is
going wrong here? I do not trust my
> > results now.
> > > >
> > > > Furthermore, is it possible
(and if so, how?) to extract the average
> > > > values of exactly the same
cluster, but in an independent group not
> > > > used in the analysis, for
post-hoc comparisons in SPSS?
> > > >
> > > > Thanks,
> > > >
> > > > Maaike
> > > >
> > > >
> > > >
_______________________________________________
> > > > 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:
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@nmr.mgh.harvard.edu
> > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
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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: 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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