Hello,
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]
- create_study - create an output area for everything
- import_bids - read the data in your bids folder and get Qunex to identify file types and assign numbers (nii folder)
- setup_hcp - reorganize BIDs data as hcp style organization (CinaB structure) so that it can be ingested into the pipelines.
- 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.
Thanks,
Lexi