Ye,

If you use the DOSS model as Doug suggested, you have will not have a column of 0s in the matrix. However, the group columns become the covariate-adjusted thickness in each group  (e.g. thickness at the mean years of meditation across everyone) - which doesn't make sense as non-meditators will always have 0 years.

What I would suggest is to mean center the covariate based on the two meditator groups and keep the the non-meditator group at 0. This will then make the meditator group means be at the mean years of the two groups and compare to the non-meditator group. This should work as I presume that you are adding the covariate to account for the differences in years of meditating.

Hope this helps.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Sun, Sep 15, 2013 at 5:42 PM, ye tian <tianye730@gmail.com> wrote:
Dear Doug,
 
I am afraid that I don't see a difference between fsgd file and customized design matrix in this case. If I were to set up my own design, the matrix would still have a column of zero's -- unless there is a trick that I don't know?
 
Thank you very much for your patience.
 
Sincerely,
Ye


On Sun, Sep 15, 2013 at 2:28 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

There is not a way to do this using an FSGD and a DODS model. It will work if you change it to DOSS (if that is appropriate). Otherwise, you will need to create your own design matrix and feed it to mri_glmfit with --X
doug



On 9/13/13 10:21 PM, ye tian wrote:
Dear Freesurfers,
 
I am studying how the practice of meditation affects cortical thickness. I have two types of meditations, and I also know for how many years each mediator has meditated. Therefore, ideally I would like my categorical factor to be meditation (control, meditation1 and meditation2), and continuous factor to be the number of years of meditation. This design, of course, has a problematic column of zeros, which corresponds to the slope of the control (a non-meditator has meditated for 0 years).
 
Does freesurfer has a way out of this problem? For example, I have came across pseudoinverse methods in literature?
 
Any suggestion is highly appreciated.
 
Thank you very much!
Sincerely,
Ye


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://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 at
http://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.



_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://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 at
http://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.