[RESOLVED] Can I run task fMRI analysis on Nifti data using a QuNex (containter)?

Can I use qunex to run task fMRI analysis on data that is purely in Nifti format? While we did collect and preprocess data following HPC guidelines, we want to compare our results that are based on permutation in Cifti space with classical volumetric analyses. Is that possible?

I haven’t found an option for this in qunex_suite-0.95.2.sif but I vaguely remember this feature being included in the HCP scripts but I can’t find it in QuNex.

JAQuent, hi!

There are two ways that you can do task fMRI analyses in QuNex. One is to use “native” QuNex functionality for estimating GLM models and using PALM to compute statistical inferences. If you go this route, you can use as input dtseries, ptseries, or “regular” volume nii.gz files, and no other change is needed, except for using PALM with ptseries data, I believe the dimensions need to be flipped before running PALM.

The other possibility is to use HCP task analysis pipeline. My understanding is that all the parameters for the pipeline can be set also through the QuNex wrapper. We would need to investigate further to see if there is anything in the way the calls for HCP are prepared that would prevent one running the analysis on volume nii.gz data if that is possible by HCP pipelines.