Dear Jana,
On Wed, 23 Nov 2022 15:45:09 +0000, Schill, Jana <[log in to unmask]> wrote:
>Dear all,
>
>I am trying to run a retrospective longitudinal VBM analysis in cat12. I am looking at approximately 50 subjects with two MRI scans - however, the time interval between scans varies widely from 1 to 15 years.
15 years are quite impressive. Was there any change in scanner or head coil? Just curious about this, because it's quite hard to keep everything stable over such a long time and scanner change would prevent that you can use that data for a longitudinal analysis.
>
>I set up the statistical model according to the guidelines in the cat12 manual, using age as a covariate (as it changes between scans and captures the differences in time intervals). However, I run into problems when estimating the model: The estimated design looks mostly black and I cannot define contrasts on it using the contrast manager (error message: 'invalid contrast'). Please see attached pictures.
Designs with varying time between the scans are not that straightforward to model: Please use that design as starting point and skip the factor group and it's definition for the conditions and also the interaction:
https://neuro-jena.github.io/cat12-help/#long_two_interact
Design → "Longitudinal data (Flexible factorial)"
Factors → "New: Factor; New: Factor; New: Factor"
Name → [specify text (e.g. "subject")]
Independence → Yes
Variance → Equal
Factor
Name → [specify text (e.g. "time")]
Independence → No
Variance → Equal
Subject
Scans → [select files (the smoothed GM data of the 1st Subject)]
Conditions → " 1 1 " [two time points]
...
Scans → [select files (the smoothed GM data of the 1st Subject)]
Conditions → " 1 1 " [two time points]
Main effects & Interaction → "New: Main effect"
Main effect
Factor number → 2
Main effect
Factor number → 1
Covariates
define here age for each time point and subject...
The final design should look similar to the last example here, except that there is just one group and the first column defines the time points and the 2nd age as covariate with two varying values for each subject:
https://neuro-jena.github.io/cat12-help/#long_contrast
The contrast should be then set:
0 -1 (i.e. atrophy over time)
Best,
Christian
>
>My questions are:
>1. Can I use age as a covariate in this setup and will it achieve what I want to achieve by using it (accounting for inter-scan time intervals).
>2. If not, what would be the correct way to set up the statistical model?
>3. What are possible reasons for the mostly black design matrix?
>
>Thank you,
>Jana
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>
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