Clarification re Amygdala task fMRI IDP (brain MRI)
Hello,
I'll soon be running some analysis on UKB task fMRI data. We're planning to look at activation in several regions of interest (ROIs), including in the amygdala. Since we want to look at activation in the left and right amygdala separately, we'll need to re-run FSL Featquery analysis rather than relying on the existing IDP 25052 - '
Median BOLD effect (in group-defined amygdala activation mask) for faces-shapes contrast'
I have found the amygdala mask I believe was used for this IDP [labelled tfMRI_mask5a.nii.gz ("Faces-Shapes" in amygdala)] by downloading the Online Resources here. The masks corresponding to mask5 and mask5a are described in the Brain Imaging Documentation as:
* 5 (Faces-Shapes group-level fixed-effect z-statistic, threshoded at Z>120)
* 5a (Faces-Shapes group-level fixed-effect z-statistic, threshoded at Z>120, and further masked by an amygdala-specific mask).
However, inspection of these masks in FSLEyes shows that the amgydala in mask5a (in green in the below picture) is actually far larger than the amygala implicated in mask5 (in red), which suggests that 5a was not the result of masking after thresholding. Was a more liberal threshold applied to the contrast to generate the 5a amygdala mask? Am I not interpretting these files correctly? Any advice would be much appreciated!
Many thanks,
Nick Souter
Comments
4 comments
Hi Fidel Alfaro Almagro & @...,
Nicholas' logic example does seem to indicate that the mask 5a thresholding isn't a sub-threshold of mask5. I've read the documentation and have come to the same interpretation.
Thanks,
Ollie
Hi Ollie and Nick,
We have just checked the original scripts that generated those masks and I am afraid there is a typo in the documentation. The group-level Zstat mask for 5a was not thresholded with Z>120, but with Z>50 (and later, masked with an amygdala specific mask coming from the Harvard-Oxford atlas). That would explain why the mask is larger in the amygdala area.
The reason was of course that activation (in particular this activation contrast) is generally less strong in the amygdala.
We will update the documentation with these corrections. Thanks for bringing it up.
Fidel & Steve
Thanks guys! Much appreciated.
Hi all,
This makes sense, thank you for the clarification!
Nick
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