Hi John,

What I mean is there could be a bias in your study design if 99% of group 1 have three or more time points and 99% of group 2 have only two time points. This is something you should check. If distributions are approximately similar, you’d be fine. LME can be used in either case. If there is any biases (also age, gender etc) you’d probably want to control for it via additional co-variates in your LME model.

Best, Martin

On Jan 28, 2016, at 1:12 PM, John Anderson j.anderson@publicist.com wrote:

Thanks a lot D martin for your quick answer. Regarding my patients I have two groups but the subject in every group have differnt time points. i.e Group-patients 1: I have 100 patients some scanned three times and some four times the rest at least two times. Group-Patients 2: is consisted of 75 patients some also some scanned three times and some four times the rest at least two times.

Is LME -- mas usnivariate still workable with out a bias ?

Bests, John

Sent: Thursday, January 28, 2016 at 6:51 AM From: "Martin Reuter" mreuter@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate Hi John,

you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3.

You can compare the atrophy across these two groups easily with LME. Or you can also test if the rate is different from zero in each individual group.

You will never be able to compute atrophy rates for your control group (as you only have a single time point for them) so you cannot compare with them either.

Best, Martin

On Jan 28, 2016, at 12:23 PM, John Anderson <j.anderson@publicist.com x-msg://92/j.anderson@publicist.com> wrote:

Hi Dr Martin, I have two groups of patients and one group of controls. The patients scanned multiple times but the number of time points is different between the subjects. The controls have only one time point.

I aim to :

1. I wanted to study the changes in cortical thickness over time in each group of patients.
2. I wanted to compare the change in cortical thickness between patients and controls over time.

I followed wiki and I choose LME to run the analysis. My questions are:

1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.
2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach.

Bests, John _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu x-msg://92/Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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

Dear FreeSurfer experts,

I hava a question regarding rerunning the recon-process. I have cases where I do manual edits on a brain and only set a few control points on one hemisphere but white matter edits on the other. I would then run the -cp flag for one hemisphere and the -wm flag for the other. My question is, can that happen simultaneously, i.e. in different terminals or should I do one after the other because of some sort of interferences?

Thanks, Clara

Hi Clara

the -cp and -wm both get run by -cp. So run that until the volume stream is done and the orig surfaces are created (or just before if you want), then run the perhemi I think.

cheers Bruce

On Fri, 12 Feb 2016, Clara Kühn wrote:

Dear FreeSurfer experts,

I hava a question regarding rerunning the recon-process. I have cases where I do manual edits on a brain and only set a few control points on one hemisphere but white matter edits on the other. I would then run the -cp flag for one hemisphere and the -wm flag for the other. My question is, can that happen simultaneously, i.e. in different terminals or should I do one after the other because of some sort of interferences?

Also, I was wondering if it is possible to save surfaces from a BASE under a different name, run the recon-process again and compare the new surfaces with the old ones and then pick, if they are better, the old ones to go on to calculate the LONGs?

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