Hi Jodie, are you familiar with mixed effects models? If not I would recommend you include a biostatistician. What I mean (and you can do this in the matlab code, no need to include it in the qdec file) is to use a piecewise linear model.
So for a subject with visits at 0, 0.4 and 0.9 years you would have this design matrix: 1 0 0 1 0.4 0 1 0.9 0.5 your model could be like this: Y_ij = beta0 + b_i + beta1 x_ij + beta2 z_ij +e_ij (i is subject index, j is time point: 1,2,3) where you have a random effect b_i for a subject specific intercept, x_ij is years and z_ij is the third column in your matrix: z_i1 = 0 z_i2 = 0 z_i3 = x_i3 - x_i2 for hypothesis testing contrast, see my email below. Best, Martin On 05/12/2014 01:14 PM, Jodie Davies-Thompson wrote: > Hi Martin, > > Thanks for your reply. I'm not entirely sure what you mean (sorry - I'm new > to this!). Do you mean something like this? > > For examining an increase between timepoint 1 and 2, but the same between > timepoint 2 and 3? > > fsid fsid-base years years-to-years > Day1 base 0 0.4 > Day2 base 0.4 0.4 > Day3 base 0.8 0 > > All the best, > Jodie > > > > Message: 6 > Date: Fri, 09 May 2014 16:52:25 -0400 > From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] nonlinear models in longitudinal analysis > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <536d4009.7030...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Jodie, > > 'years' should contain the real time between time points (usually, > unless you have test-retest where time is irrelevant, or different task > that can be ordered as you like). For what you are trying to do you > should use linear mixed effects models with a piecewise linear setup. > This will allow you to estimate a slope before and after timepoint 2 and > compare those slopes. > Your design matrix would probably have the column of 1, years and a > column with > years-years(at tp2 of that subject) if that value is positive > 0 otherwise > > Testing if the coef of the 3rd column is > 0 is asking if the slope > increases in the second interval. Not exactly what you want, but close > and of course you can test if the slope in interval 1 is different from > zero (second column) and if the slope in interval 2 is different from > zero ( 0 1 1, ie the sum of the last two columns). > > Best, Martin > > On 05/08/2014 03:48 PM, Jodie Davies-Thompson wrote: >> Dear Freesurfer experts, >> >> I am attempting to do a longitudinal analysis of cortical thickness with 3 >> timepoints. So far, I have successfully completed the analysis for >> long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to >> timepoint 3, and a linear increase for timepoint 1 to 2 to 3. >> >> However, I am primarily interested in finding regions which show a) an >> increase between timepoint 1 and 2, but no difference between 2 and 3, and >> b) no difference between timepoint 1 and 2, but an increase between 2 and 3. >> >> Would the correct way of 'modelling' these two in the qdec file be: >> >> a) >> fsid fsid-base years >> day1 base 0 >> day2 base 3 >> day3 base 3 >> >> and b) >> fsid fsid-base years >> day1 base 0 >> day2 base 0 >> day3 base 3 >> >> All the best, >> Jodie >> >> - >> --- >> Jodie Davies-Thompson, Postdoctoral Fellow >> Department of Ophthalmology & Visual Sciences >> UBC/VGH Eye Care Centre >> 2550 Willow Street >> Vancouver, BC, V5Z 3N9 >> Canada >> Tel: 604-875-4111 ext 69003 >> > - > --- > Jodie Davies-Thompson, Postdoctoral Fellow > Department of Ophthalmology & Visual Sciences > UBC/VGH Eye Care Centre > 2550 Willow Street > Vancouver, BC, V5Z 3N9 > Canada > Tel: 604-875-4111 ext 69003 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.
