[RESOLVED] How to setup HCP pipeline for BIDS format data


We are gearing up to process GE data that is organized in BIDs format. We have been attempting to run the following commands [our understanding in brackets]

  1. create_study - create an output area for everything
  2. import_bids - read the data in your bids folder and get Qunex to identify file types and assign numbers (nii folder)
  3. setup_hcp - reorganize BIDs data as hcp style organization (CinaB structure) so that it can be ingested into the pipelines.
  4. hcp_pre_freesurfer - run pre freesurfer pipeline on the the CinaB structure.

a and b run without error and correctly map bids’ anat folder to the nii folder in our study folder, however setup_hcp is returning empty folders with no error messages.

Do we need additional steps to adapt BIDS format data to hcp pipeline? Or import_bids can automatically do that?

Our setup_hcp command:

${QUNEXCOMMAND} setup_hcp \
            --sessionsfolder="${StudyFolder}/sessions/CONN008_BL/nii" \
            --sessions="CONN008_BL" \
            --hcp_filename="userdefined" \
            --hcp_folderstructure="hcpls" \

According to the manual, we need a source file named session_hcp.txt. To have this file we need to extend our session.txt with the existence of hcp_mapping.txt.

Where should we go look for the hcp_mapping.txt? We don’t have this file in our default location.


Hi Lexi,

Welcome to QuNex forums! Yes, to map the data from QuNex folder structure to HCP folder structure you need a HCP mapping file. This files tells QuNex additional information about the files you just onboarded. The thing is that not all information can be reliably extracted from images themselves or from supporting files. An example mapping file can be found in our quick start (QuNex quick start using a Docker container — QuNex documentation). If you are not able to resolve this on your own, please upload your session.txt and the mapping file you prepared and we will help you out.


Thank you so much Jure! It worked.

Great, glad I could help!