I have an fMRI overlay that was output from meta-analysis software, so I only have the .nii results file, no raw data. I would like to view this file in conjuction with the AAL3 atlas.

  • I usually use FSL but I cannot work out how to get the AAL3 atlas to work in FSL (I've managed to get the aal3v1.nii file into the right place but when I try to select it in the atlas pane, it hangs).

  • I'm less familiar with MRICron but I did manage to get the AAL3 atlas to load. I cannot, however, get the brain region labels to show and it's the labels that I need.

  • I have never used SPM before. I've tried following several instruction manuals/tutorials but cannot even work out how to view my overlay. The AAL3 instructions are for SPM and talk about setting up contrasts and so on but I only have the .nii file - I don't have any data to analyse.

Can anyone offer an idiot's guide to viewing an overlay with the AAL3 atlas, please, in any program? I've spent so many hours trying to work this out but I'm totally lost.


1 Answer 1


I think to use the MRIcorn is the easiest way, You can put the AAL3v1.nii.gz and AAL3v1.nii.txt into the mricron-templates folder. enter image description here

by the way which software you use to do fMRI meta-analysis?

best, Hui Zheng Shanghai Mental Health Center

  • $\begingroup$ Thank you. That's great. I'm using GingerAle to do a meta-analysis but I understand SDM may be used instead. brainmap.org/ale sdmproject.com $\endgroup$
    – PCS
    Sep 7, 2020 at 14:57

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