Hi Doug,
Thank you for such a prompt response. Just to be clear you are recommending
that I manually create the matrix file right?
If so I want to ensure that I am understanding how to design the matrix
file properly.
Let's imagine that the first participant is a control and is 13 and the
second is a patient and is 15. My understanding is that the matrix file
would be as follows:
0 0 0 0 0 0 0 0 13 0
0 0 0 0 0 0 0 0 0 15.
-Tim
Previous correspondences are below:
You'll need a regressor for each of the 8 classes you describe below.
You can use mri_glmfit to generate this (Xg.dat file)
You'll need two more regressors for age, one for each diagnosis. If a
subject (ie, row) is a control then the two values will be AGE 0. If the
subject of the row is a patient, then the two values will be 0 AGE. You
can then set up a Controls-Patients age (ie, interaction between dx and
age) contrast like
[0 0 0 0 0 0 0 0 1 -1]
On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
Freesurfer Support,
I'd like to create a design matrix for a group analysis outside of the
DODS and DOSS models. I understand that in order to do this the -X
flag must be used. However, I have been unable to find examples of how
to do this.
I am hoping to reveal a difference in thickness or gyrification
amongst a clinical population. The data set contains two factors:
diagnosis, and study site and one covariate: age. Diagnosis has two
levels: controls, and patients. Study site has four levels, one level
for each location the data has been collected from.
What I would ideally like to do is:
Take into account offset differences amongst diagnosis and study site.
Allowing a difference in age slope amongst the diagnosis levels
Modeling the age slope as the same for the study site levels
My FSGD file is designed as follows
Class SITE 1-Control
Class SITE 1-PATIENT
Class SITE 2-Control
Class SITE 2-PATIENT
Class SITE 3-Control
Class SITE 3-PATIENT
Class SITE 4-Control
Class SITE 4-PATIENT
Variables age_at_scan
study site levels = 1,2,3 and 4
diagnosis levels = PATIENT and Control
age_at_scan = covariate age
Any advice would be greatly appreciated.
Respectfully,
Tim
--
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 tel:507-259-3434 (texts okay)
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--
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MGH-NMR Centergr...@nmr.mgh.harvard.edu
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On Tue, May 24, 2016 at 1:30 PM, Timothy Hendrickson
hendr522@umn.edu
wrote:
>
> Freesurfer Support,
>
> I'd like to create a design matrix for a group analysis outside of the
> DODS and DOSS models. I understand that in order to do this the -X flag
> must be used. However, I have been unable to find examples of how to do
> this.
>
> I am hoping to reveal a difference in thickness or gyrification amongst a
> clinical population. The data set contains two factors: diagnosis, and
> study site and one covariate: age. Diagnosis has two levels: controls, and
> patients. Study site has four levels, one level for each location the data
> has been collected from.
>
> What I would ideally like to do is:
>
> 1) Take into account offset differences amongst diagnosis and study site.
>
> 2) Allowing a difference in age slope amongst the diagnosis levels
>
> 3) Modeling the age slope as the same for the study site levels
>
> My FSGD file is designed as follows
>
> Class SITE 1-Control
> Class SITE 1-PATIENT
> Class SITE 2-Control
> Class SITE 2-PATIENT
> Class SITE 3-Control
> Class SITE 3-PATIENT
> Class SITE 4-Control
> Class SITE 4-PATIENT
> Variables age_at_scan
>
> study site levels = 1,2,3 and 4
> diagnosis levels = PATIENT and Control
> age_at_scan = covariate age
>
> Any advice would be greatly appreciated.
>
> Respectfully,
>
> Tim
>
> --
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
>
--
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
