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: > > 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) > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. On Tue, May 24, 2016 at 1:30 PM, Timothy Hendrickson <hendr...@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)
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