[RESOLVED] Setup_hcp error when importing only DWI (not T1/T2) data

Issues
1

Hi!

I have unprocessed HCP DWI data that I would like to import to be able to run hcp_diffusion. I only have dMRI data in the folder that imported using import_hcp:

unprocessed
    └── Diffusion
        ├── HCD0295954_V1_MR_dMRI_dir98_AP.bval
        ├── HCD0295954_V1_MR_dMRI_dir98_AP.bvec
        ├── HCD0295954_V1_MR_dMRI_dir98_AP.json
        ├── HCD0295954_V1_MR_dMRI_dir98_AP.nii.gz
        ├── HCD0295954_V1_MR_dMRI_dir98_AP_SBRef.json
        ├── HCD0295954_V1_MR_dMRI_dir98_AP_SBRef.nii.gz
        ├── HCD0295954_V1_MR_dMRI_dir98_PA.bval
        ├── HCD0295954_V1_MR_dMRI_dir98_PA.bvec
        ├── HCD0295954_V1_MR_dMRI_dir98_PA.json
        ├── HCD0295954_V1_MR_dMRI_dir98_PA.nii.gz
        ├── HCD0295954_V1_MR_dMRI_dir98_PA_SBRef.json
        ├── HCD0295954_V1_MR_dMRI_dir98_PA_SBRef.nii.gz
        ├── HCD0295954_V1_MR_dMRI_dir99_AP.bval
        ├── HCD0295954_V1_MR_dMRI_dir99_AP.bvec
        ├── HCD0295954_V1_MR_dMRI_dir99_AP.json
        ├── HCD0295954_V1_MR_dMRI_dir99_AP.nii.gz
        ├── HCD0295954_V1_MR_dMRI_dir99_AP_SBRef.json
        ├── HCD0295954_V1_MR_dMRI_dir99_AP_SBRef.nii.gz
        ├── HCD0295954_V1_MR_dMRI_dir99_PA.bval
        ├── HCD0295954_V1_MR_dMRI_dir99_PA.bvec
        ├── HCD0295954_V1_MR_dMRI_dir99_PA.json
        ├── HCD0295954_V1_MR_dMRI_dir99_PA.nii.gz
        ├── HCD0295954_V1_MR_dMRI_dir99_PA_SBRef.json
        ├── HCD0295954_V1_MR_dMRI_dir99_PA_SBRef.nii.gz
        └── OTHER_FILES
            ├── HCD0295954_V1_MR_SpinEchoFieldMap5_AP.json
            ├── HCD0295954_V1_MR_SpinEchoFieldMap5_AP.nii.gz
            ├── HCD0295954_V1_MR_SpinEchoFieldMap5_PA.json
            └── HCD0295954_V1_MR_SpinEchoFieldMap5_PA.nii.gz

The data gets copied to /qunex/study_folder/sessions/HCD0295954_V1_MR/hcpls/Diffusion using import_hcp, however setup_hcp throws the error


===> ERROR in completing setup_hcp:
     No files mapped
     No files were found to be mapped to the hcp folder [/qunex/study_folder/sessions/HCD0295954_V1_MR]!
     Please check your data!

Is it necessary to include any additional files in the RAW_DATA folder in order for this to work?

Best regards and thank you in advance,
Karin

2

Hi Karin,

Could you please provide full command calls for both import_hcp and setup_hcp. Also, please check if session.txt and session_hcp.txt exist in /qunex/study_folder/sessions/HCD0295954_V1_MR and provide the contents here. This will help us out with figuring out what happened.

Jure

3

A side remark is that hcp_diffusion does not work only on diffusion data but needs structural as well. You need to complete the FreeSurfer pipeline (hcp_pre_freesurfer, hcp_freesurfer and hcp_post_freesurfer) to be able to run hcp_diffusion.

Jure

4

We were unable to reproduce the above error. In our case onboarding DWI only data worked. However, we have added an error message that if you try to run HCP Pipelines without appropriate data (e.g., the Diffusion pipeline without structural data), QuNex will tell you that it does not work.