Help with running group analyses in halfpipe

[EmeseK]

Hi all,

I have preprocessed and ran my first-level analyses using halfpipe and after checking all the quality output I would like to run some group-level analyses now. However, I'm not sure how to proceed now:

• Is there a way to input the first-level output and only run the higher levels? Or do I always need to re-run the first-level analysis? or even re-run the preprocessing?
• If not, would it be possible to input halfpipe first-level output into fsl directly?

Best,

Emese

[HippocampusGirl]

Hi @EmeseK,

• You can skip the first level processing and only run the higher level by adding the command line flag --only-model-chunk to the end of the command you use to start HALFpipe

• It is possible to input the results from HALFpipe into FSL directly. All the statistical maps you need are in the derivatives/halfpipe folder. Slide 15 of https://osf.io/3hdex shows some information about the file names of the statistical maps

Best,
Lea