Hi John,
a few answers, maybe Jorge has more details when he get’s back from travel.
1. if you look at the wiki: Y = M(:,7:9), therefore these are the left and
right hippo-volumes. So the plot shows the total hippocampal volume.
2. I think you need to plot them individually. Probably you won’t see anything
anyway if it is plotted on top of each other. You can sum left+right if you
like or look at hemispheres independently.
3. There should be as many lines as groups. I am not sure about the order. The
script uses a call to ‘unique' to find unique groups, so I guess it is the
order in which groups appear in the qdec file. The order of the colors is:
colors = {'b','k','g','c','m','r','y’}; (it starts with ‘k’ and wraps around at
the end)
Take a look at the lme_lowessPlot.m file, it should be easy to add a legend to
the plot, by copying and editing the file.
4. that parameter smoothes the data. It calls smooth with the ‘rlowess’
parameter. See the help of ‘smooth' or play around with the parameter. The goal
of the plot is to see a trend of the data, so smooth away small bumps but not
the main signal.
Best, Martin
> On Jan 2, 2016, at 10:57 AM, John Anderson <j.ander...@publicist.com> wrote:
>
> Hi Freesurfer experts,
> I am working on a logitudinal data analysis using freesurfer pipeline. I
> followed all the steps like in WIKI and the analysis was great. Kindly I have
> the following questions:
> 1. In wiki "http://freesurfer.net/fswiki/LinearMixedEffectsModels
> <http://freesurfer.net/fswiki/LinearMixedEffectsModels>"-- in the example
> mentioned there, the command "
> lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));"
> What is the Y(:,2) refer to ?
> 2. Can I plot multiple measures at the same time ( for example if I have in
> my qdec table multiple columns for multiple measures ( left precentral gyrus
> cortical thickness, right precentral gyrus cortical thickness, LH mean
> thickness , RH mean thickness) can I plot all these measures at the same time
> instead of running the previous command multiple times?
> 3. If I have three groups in my qdec table. The previous command line is
> plotting three lines. Are these lines in th esame order of the groups in qdec
> tables?
> 4. The BW in this command was chosen 0.7 and the default is 0.6 how can I
> choose this number correctly?
>
> Thanks for your support!
>
>
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
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