Run cwas pipeline with cpac with already preprocessed fMRI data

Hi, neurostarts experts :slight_smile:

I have a question on running cwas (one of group-level analysis pipelines) thru cpac with already preprocessed fMRI data (by fMRIprep).

I tried to figure out what I should do to run CWAS pipeline but having a hard time understanding overall steps (what to do first, second and so on).

I have created data_settings.yml and data_config.yml files.

So, I guess it’s time to select my pipeline that will run cwas without any preprocessing steps.

(this page) told me to add the following lines to my file with appropriate paths.

runCWAS = [0] cwas_roi_file = ‘/path/to/cwas_mask_file’ cwas_regressor_file = ‘/path/to/cwas_regressor_file’ cwas_regressor_participant_column = 'ID cwas_regressor_columns = [‘FIQ’, ‘VIQ’, ‘PIQ’] cwas_permutations = 500 cwas_parallel_nodes = 3

I want to make sure where exactly should I add these lines since I don’t need any preprocesssing. I thought cpac gui will make my head clear but the page somehow reports an error (Something went wrong!) everytime I try to acccess.

Is it okay to manually create and run pipeline.yml that only contains the upper lines (since I don’t need any preprocessing steps) to run cwas?

And I found MDMR workflow developer documentation) where there are 2 relevant source codes (CPAC.cwas.pipeline & CPAC.cwas.cwas).

I want to check if I should run CPAC.cwas.cwas first and then run CPAC.cwas.pipeline (seems like the latter is run with input from the former) and that if that’s all for cwas analysis.

So, I wonder if there’s anyone who can explain sequential steps to run cwas in this case…

I’ll be so grateful for any of your help.

Thank you in advance and hope you have a great day!!!

Susan.

Hello Susan!

My name is Diego and I have been working with C-PAC to update the deprecated group analysis parts in C-PAC. Specifically I have been working on the changes to have CWAS/MDMR function with the BIDS preprocessed participant data. I can share with you my fixes for the code (GitHub - diegoaper/C-PAC_MDMR-Group_Runner: Configurable Pipeline for the Analysis of Connectomes) however use this with caution as we are still testing and trying to make sure all the bugs are removed before committing the changes. If you are still interested in working with my changes I am more than happy to help troubleshoot as you go. We are also updating the documentation as we go along.