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
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, create your matrix manually.
Those matrix lines are not quite right. The ages are in the correct column, but you need a 1 somewhere in columns 1-8 to indicate the class (ie, site/dx) that the subject is in.
On 05/26/2016 12:57 PM, Timothy Hendrickson wrote:
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)
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 tel:617-724-2358 Fax:617-726-7422 tel:617-726-7422
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On Tue, May 24, 2016 at 1:30 PM, Timothy Hendrickson <hendr522@umn.edu mailto: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 <tel:507-259-3434> (texts okay)-- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Timothy Hendrickson