External Email - Use Caution Thanks, Kersten.
I am sorry, I didn't see your response in the FS blog. I will go through it once and let you know! Once again thanks a lot for your kind mail! With regards Vittal On Thu, Dec 10, 2020 at 6:35 PM Diers, Kersten /DZNE <kersten.di...@dzne.de> wrote: > Hello Vittal, > > I am (again) attaching my response to your message. This response has been > on the freesurfer list since Nov 30, maybe you did not see it? > > Best, Kersten > > *From:* Diers, Kersten /DZNE > *Sent:* Monday, November 30, 2020 6:27 PM > *To:* Freesurfer support list > *Subject:* Re: Longitudinal pipeline > > Hello VIttal, > > thanks for the info about the design. > > You wrote before that the Matlab variable X (i.e., the design matrix) has > a dimension of 47x6. X is a translation of the study design into a > numerical matrix, which is part of the statistical model. In your case, I > assume that he first column is a vector of ones (i.e. the > intercept/constant of the statistical model), and that the other columns > reflect the numerical data in the table that you sent, in the same order. > Correct me if I am wrong. > > Now, the contrast "matrix“ specifies the questions that you want to ask to > the data, i.e. the effect of a certain variable (or sometimes combinations > of variables) onto the outcome variable Y. I put "matrix" in quotes, > because in many cases a simple vector is sufficient; contrasts need not > necessarily be specified as a matrix, and contrasts specified as a matrix > are typically more complex than those specified by a vector. > > In any case, the contrast vector/matrix needs to have as many > elements/columns as there are columns in X, because the elements/columns > oft the contrast vector/matrix will be matched with (and therefore need to > correspond to) the columns of X. I.e. the nth element/column in your > contrast vector/matrix refers to the nth predictor variable in the > statistical model, i.e. the nth column of X. There are 6 columns in X in > your case. > > The entries in the contrast vector/matrix represent weights that you > assign to each variable in order to test for its effect. One often (but not > always or necessarily) uses +1 to test for a positive relation of the > chosen variable on Y, -1 for a negative effect, and zero for not > considering a variable for a given contrast. Therefore, the simplest > contrast is a vector with a single non-zero entry, and this already allows > for the testing of effects. In other cases, contrasts can have more than > one non-zero entry, or can be formulated as a matrix, but we don’t need > this at the moment. > > The major issue with your design in its current form is that you will not > be able to distinguish effects of time from effects of treatment, due to > the absence of a control group. This precludes, as far as I can see, a > clear interpretation of any changes in Y that you might observe. If you > still want to go ahead and test the time/treatment effect, just set the > corresponding element of the contrast vector to +1 or -1. > > Best, > > Kersten > > Am 10.12.2020 um 09:10 schrieb vittal korann <vittalkor...@gmail.com>: > > Hi Kersten > > Thank you for kind response. > > I think we need to talk about the design matrix X first (sorry, I did not > look at your xlsx file; I think it's probably better to send simple csv > files if at all). > I attached longitudinal data in csv format. > > Besides the covariates that you mention, the matrix needs to contain an > intercept, a variable for ?time?, a variable for ?group? (assuming you have > a control group also), and a group-by-time interaction term in order to > asses differential change over time (again, if you have a control group). > I do not have a control group. Right now I have only schizophrenia > patients who underwent 2 scans: first is baseline and second one is after 3 > months of yoga therapy. Wish to know the how can I proceed with my availabe > data. > > Just to make sure: ?age? should be ?age at baseline? (i.e. constant across > time per subject), otherwise it will be confounded with time. > Yes, I used same across the study. > > Could you review (and possibly adapt) your design matrix X with respect to > which columns it contains, and write it in the reply? > I tried but couldn't get there. > > Any help would be greatly appreciated! > > Thanks, > Vittal > > > > > > <longitudinal_data (1).csv> > > > -- > Kersten Diers > Image Analysis Group (AG Reuter) > German Center for Neurodegenerative Diseases (DZNE) > B.1.114 | Building 99 | Venusberg-Campus 1 | 53127 Bonn | Germany > https://secure-web.cisco.com/1g0Gvv7AJ1xY5h4Q2uX7HwpMsjqaKvF-OfFFqsr1eLA7VETRa_HPhQsNAEHYJPHguaqtB-gt1W21crc9EJ--iH0CnAxOky9Y44t8Z503LiBVjND2BHbw498sQT1Qdq1UfXhk5MXkEm0QL7pObzuzbMmE_x1CqlGLWzCQdhAJfw0nG1AD5N4UG94tnIc-DBBr0cKS2ZDVgAqDhgsbAeDoqH2nfjGDaGS53Tc0I6Vtw2il5JnQs3usk03xXD_0eu4ePnCqQHy2VG_xxELqohCpxCQ/https%3A%2F%2Fwww.dzne.de%2Fen%2Fsites%2Fbonn%2Fresearch-groups%2Freuter.html > Phone: +49 / 228 / 43302 - 381 > >
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