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
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
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.eduwrote:
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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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.eduwrote:
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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Just remove that column. You don't need it or want it. doug
On 9/15/13 11:42 PM, ye tian 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 mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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@nmr.mgh.harvard.edu
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Douglas Greve -
MCLAREN, Donald -
ye tian