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How to set up an ANOVA for ROI analysis

Feb 17, 2018 6:36 AM
(3279 views)

Apologies in advance to seasoned JMP users; this is a newbie question.

I have a dataset of anatomically-derived brain ROIs measuring fractional anisotropy (FA). There are a total of 20 ROIs, some of which are 2nd order (derived from the others). My main factor is group (normal vs dementia). For the FA analysis, I would also like to control for size differences between the SAME ROI in the 2 groups (I have ROI size, in mm for each one). Also age and sex. How do I set up the ANOVA in JMP13? Data structure is as follows:

Subject 1: group, ROI1_FA, ROI2_FA, ROIn_FA, ROI1_size, ROI2_size, ROIn_size, age, sex

Subject 2: group, ROI1_FA, ROI2_FA, ROIn_FA, ROI1_size, ROI2_size, ROIn_size, age, sex

Subject x: group, ROI1_FA, ROI2_FA, ROIn_FA, ROI1_size, ROI2_size, ROIn_size, age, sex

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Re: How to set up an ANOVA for ROI analysis

Are the ROI measurements for each subject considered independent responses?

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No they're not. These ROI measures will be highly correlated, as they are different-but-adjacent brain regions from the same individual.

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Re: How to set up an ANOVA for ROI analysis

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Re: How to set up an ANOVA for ROI analysis

Created:
Feb 19, 2018 9:47 AM
| Last Modified: Feb 19, 2018 9:51 AM
(3229 views)
| Posted in reply to message from neurodoc 02-19-2018

Thanks for your reply. This note should be helpful to you in setting up your analysis. There are three different approaches for you to consider.

As for the size, I don't know enough about your field to suggest anything but the most obvious normalization approaches, such as ratio (ROI / size). You might be able, though, to use it as a covariate if you use the 'split-plot' approach described in the note.

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Re: How to set up an ANOVA for ROI analysis

Thank you, that article was definitely helpful. I am certain that what I was looking for was the Mixed Model "personality," and what I was missing was knowledge of the "stack" command under the Tables menu, which allowed me to restructure my data to fit the method. I am now faced with another, higher-level question, which is the choice of repeated covariance structure for my data. I suspect I need one of the 4 "spatial" options, but this is just a hunch, and I certainly don't know which of the 4 to select, nor which "Type" is best for these data, nor what is meant by the required "Repeated" input. Is there a page that discusses these options?

All in all, what would be most helpful would be to find a discussion somewhere of how to use JMP with MRI (or similar imaging) data. Is there such a page, or group available?

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Re: How to set up an ANOVA for ROI analysis

bump.

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Re: How to set up an ANOVA for ROI analysis

You do not seem to have the spatial information to fit a spatial model using Mixed Model. Here is an example of fitting such model. https://www.jmp.com/support/help/13-2/Spatial_Example_3a_Uniformity_Trial.shtml#1264182

However, with the data you've collected shown above and stacked where there are Subject column identifying subjects and Repeated column identifying the sequence of ROI_FA, you can run the analysis of repeated measures using Mixed Model. ROI_size as well as age and sex enter the model as fixed effects. To start, try some of the simpler covariance structures https://www.jmp.com/support/help/13-2/Fit_Model_Launch_Window_2.shtml

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