Resting state fMRI - detection DMN with seed in hippocampus:
I would like to set a maximum pixel cluster size as threshold to compare seed based analysis results of data sets made on different scanners and with different head coils. This is not possible with the REST toolbox. Any other suggestions? Thanks in advance.
Hi Stephanie,
The statistical thresholding of rs-fMRI data is always a bit tricky: there are multiple ways to do it, and no clear consensus. To determine a minimal cluster size, I used the AFNI toolbox, and especially their 3dClustSim program; it uses Monte Carlo simulations to determine a minimal cluster size which leads to a global alpha value you can specify (usually 0.05), based on the voxel-level statistical threshold (p-value) you use. Attached is the link to the detailed program description.
ex: with a p 205 voxels...
Does that help? Is that what you wanted?
http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dClustSim.html
I am afraid that you have to do it in AFNI for visualization purposes if you want. However, you can do your calculations with rest and then implement the cluster-size in SPM when you go to "check results" and chose no FWE correction... Does that help?
Multiple correction for result representation?
AlphaSim correction can be done on toolkit of REST: Utility-->REST AlphaSIM, which is not dependent on what's the analysis you done. seed-based FC, ALFF, task-state activation or else.... why emphaaaaasize RS fMRI seed based analysis?
I also need to determine the minimum cluster level with Monte Carlo simulation, but I don't know to use the AFNI program at all. Is there any way I can do this analysis without using AFNI?
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