[RESOLVED] Task fMRI processing using qunex

Hi, I was looking into the commands for task fMRI processing and noticed that there are ways of doing it:

The first seems simpler and follows more closely the description in the HCP pipelines github page. The second one seems more involved and need creation of ‘conc’ and ‘fidl’ files. I was wondering what are other differences between these two and what are the main advantages of choosing the more involved process. Thank you.


Estephan, hi!

As you have noted, the two ways of running task analyses come from different perspectives or starting points, and it mainly depends on which way of running analyses you are more familiar with. One way of running task analyses is to make use of the HCP task fMRI analysis pipeline. That pipeline starts from HCP preprocessed data in HCP folder structure and makes use of FSL to run task analyses. If you are familiar with and prefer FSL and/or would like to run analyses similar to ones used with HCP data, then that might be the better options. The other possibility starts with data mapped to QuNex folder structure, it uses “fidl” event files and “conc” files that specify which bolds and in what order are to be analysed (there is a create_conc function that simplifies creation of conc files, and there are functions that help join fidl files for individual bold runs and check the event structure), and it makes use of QuNex’s own GLM engine and support functions. The QuNex GLM engine has been developed for easy assumed HRF and unassumed modeling of events and it provides an easy and flexible way to include behavioral coregressors. It provides additional functions for extracting events of interest from the GLM files and ROI statistics, and it plays nicely with PALM for second level analysis. It supports working with volume, dense and parcellated bold data. Each approach has its own advantages and limitations. We like it because once fild files are created, it is quite easy to run different models just by adjusting the event string, and the support functions make it easy to work with group data.

If you would like more information about the HCP task pipeline, the HCP repository and mailing list are the best resources. If you would like more information about QuNex tools for task analysis, feel free to ask.

All the best,


Very helpful Grega, thanks for the explanation.