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 rakamaitra@yahoo.com To: Douglas N Greve greve@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 greve@nmr.mgh.harvard.edu To: raka maitra rakamaitra@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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