Dear Doug
Many thanks for your reply.
Freesurfer does accept the design matrix you suggested.
For the following design matrix
1.0000 0 0.5000
1.0000 0 -0.5000
0 1.0000 0.5000
0 1.0000 -0.5000
The contrast 0 0 1 is meaningful for effect of two positions.
But if I extrapolate it to 3 positions
1.0000 0 0.6700
1.0000 0 -0.3300
1.0000 0 -0.3300
0 1.0000 0.6700
0 1.0000 -0.3300
0 1.0000 -0.3300
A contrast 0 0 1 would only test position 1 > (position 2 and 3)
If my understanding is correct, then for effects of other positions I would
have to repeat the above.
And if so, then is there any way I could combine the separate results ?
Thanks in advance for your time
Raka
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: raka maitra <rakamai...@yahoo.com>
Cc: freesurfer_mailing_list <freesurfer@nmr.mgh.harvard.edu>
Sent: Tue, January 19, 2010 7:11:29 PM
Subject: Re: [Freesurfer] Fw: manually specifying design matrix
It would probably be more like this:
1.0000 0 0.5000
1.0000 0 -0.5000
0 1.0000 0.5000
0 1.0000 -0.5000
The 1st col codes subject 1. The 1st row is the 1st measure of subject 1
and the 2nd row is the 2nd measure of subject 1.
doug
raka maitra wrote:
> Hello
>
> Sorry for reposting again.
> Would really appreciate a feedback on the following mail.
>
> Thanks in advance for your time
> Raka
>
>
> ----- Forwarded Message ----
> *From:* raka maitra <rakamai...@yahoo.com>
> *To:* Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> *Sent:* Fri, January 15, 2010 9:34:02 PM
> *Subject:* Re: [Freesurfer] manually specifying design matrix
>
> Thank you Doug.
>
> I am trying to create a design matrix for repeated measures anova.
>
> Lets say subjects A and B have been measured at sitting and standing
> positions.
> As the same subjects have been measured at the same positions, hence
> both the factors i.e subjects and positions are fixed factors.
> Hence a design matrix exploring the within subject effects of
> positions would be
> 1 0 1 0
> 0 1 1 0
> 1 0 0 1
> 0 1 0 1
> The first two columns are position and the last two are the subjects.
>
> But mri_glmfit does not accept this design and I get the following
> error message:
>
> 'Matrix condition is 1e+08
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.'
>
> Looking forward to your suggestion
> Thanks in advance
> Raka
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> *To:* raka maitra <rakamai...@yahoo.com>
> *Cc:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Thu, January 14, 2010 7:05:28 PM
> *Subject:* Re: [Freesurfer] manually specifying design matrix
>
> If you specify it manually, you don't specify groups, etc, or pass an
> fsgd file. You just create your design matrix pass it to mri_glmfit
> directly with the --X flag.
>
> doug
>
> raka maitra wrote:
> >
> > Hi all
> >
> > I want to specify a design matrix manually.
> >
> > In the usual pipeline for analysis in freesurfer, one specifies the
> > groups, regressors in the fsgd and then when mri_glmfit is run, it
> > creates the design matrix.
> > For eg if I have two classes with 3 subjects each, in my fsgd,
> > mri_glmfit would create the following design matrix
> > 1 0
> > 1 0
> > 1 0
> > 0 1
> > 0 1
> > 0 1
> >
> > If I want to specify the above design matrix manually, how and where
> > do I specify the groups, regressors ?
> >
> >
> > Thanks in advance
> > Raka
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
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> > 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
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
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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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