Hello! I am intending to process the HCP raw diffusion data but I do not have to process the structural data first as I already have the preprocessed structural data (and all the other outputs from the preprocessing) that was done by the HCP team. Is it possible to import both processed and unprocessed data into QuNex? Do I just combine both processed and unprocessed data into a single folder (for each subject) and then use the import_hcp command?
Thank you!
Hello!
QuNex currently does not provide a command that would enable single-step importing of processed HCP data. If there is a need for that functionality in the community we would consider adding it in the future. Currently, the way to make use of the preprocessed data would be the following.
1/ use import_hcp to import the unprocessed data
This step would populate the nii subfolder with the raw files and it would create the session_hcp.txt files that are necessary for compiling a batch file that can then guide further processing within QuNex.
2/ use setup_hcp to prepare hcp folder for each session
This step generates and populates the sessions/<session id>/hcp/<session_id> folder with the unprocessed data to prepare it for further processing using HCP pipelines.
3/ copy or move the processed data to the hcp folder
This step would need to be done “manually” or using a custom script, which would for each session map the processed data to the sessions/<session id>/hcp/<session_id> folder.
With these three steps done, you could continue processing and run the steps that have not yet been completed using QuNex.
An alternative would be to write a custom script to skip steps 1/ and 2/ and generate all the necessary folders and files in the process. I would only advise this if you have a thorough understanding of the files that need to be generated and the underlying folder/file structure.