Hi all,
I meet a problem while importing HCP data. The error shows:“Could not parse file”. Do I miss some naming specifications or extra settings?
qunex_container import_hcp \
--sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
--sessions="${SUBJ}" \
--inbox="${RAW_DATA}" \
--archive="leave" \
--bind="/hdd1:/hdd1" \
--container="${QUNEX_CONTAINER}" \
--overwrite="yes"
One of my raw data folders looks like:
ehui@ehuicompute:/hdd1/qunex/cimt/validationdata/rawdata/ForProfHui/MRIdata/HOS009_pre$ ls
DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211217111856_9.json
DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211217111856_9.nii
DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211217111856_9.zip
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_10.bval
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_10.bvec
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_10.json
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_10.nii
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_10.zip
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_12.json
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_12.nii
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_12.zip
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_13.json
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_13.nii
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_13.zip
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_14.json
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_14.nii
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_14.zip
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_15.json
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_15.nii
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_15.zip
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_17.json
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_17.nii
DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217111856_17.zip
DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211217111856_24.json
DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211217111856_24.nii
DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211217111856_24.zip
DICOM_t1_mprage_we_sag_iso_20211217111856_5.json
DICOM_t1_mprage_we_sag_iso_20211217111856_5.nii
DICOM_t1_mprage_we_sag_iso_20211217111856_5.zip
DICOM_t1_mprage_we_sag_iso_20211217111856_6.json
DICOM_t1_mprage_we_sag_iso_20211217111856_6.nii
DICOM_t1_mprage_we_sag_iso_20211217111856_6.zip
DICOM_t2_space_cs_sag_20211217111856_7.json
DICOM_t2_space_cs_sag_20211217111856_7.nii
DICOM_t2_space_cs_sag_20211217111856_7.zip
DICOM_t2_space_cs_sag_20211217111856_8.json
DICOM_t2_space_cs_sag_20211217111856_8.nii
DICOM_t2_space_cs_sag_20211217111856_8.zip
Here also attached my log file:validationdata_import_hcp_2025.07.04-11.14.39.txt (46.5 KB)
Always thanks your kindly help!
Best,
Hi Acacius,
The import_hcp function is meant for importing datasets that are organized in the unprocessed HCP style way. This is an example of such organization:
HCA6086369_V1_MR
└── unprocessed
├── Diffusion
│ ├── HCA6086369_V1_MR_dMRI_dir98_AP_dir98_AP.bval
│ ├── HCA6086369_V1_MR_dMRI_dir98_AP_dir98_AP.bvec
│ ├── HCA6086369_V1_MR_dMRI_dir98_AP_dir98_AP.nii.gz
│ ├── HCA6086369_V1_MR_dMRI_dir98_PA_dir98_PA.bval
│ ├── HCA6086369_V1_MR_dMRI_dir98_PA_dir98_PA.bvec
│ ├── HCA6086369_V1_MR_dMRI_dir98_PA_dir98_PA.nii.gz
│ ├── HCA6086369_V1_MR_dMRI_dir99_AP_dir99_AP.bval
│ ├── HCA6086369_V1_MR_dMRI_dir99_AP_dir99_AP.bvec
│ ├── HCA6086369_V1_MR_dMRI_dir99_AP_dir99_AP.nii.gz
│ ├── HCA6086369_V1_MR_dMRI_dir99_PA_dir99_PA.bval
│ ├── HCA6086369_V1_MR_dMRI_dir99_PA_dir99_PA.bvec
│ └── HCA6086369_V1_MR_dMRI_dir99_PA_dir99_PA.nii.gz
├── rfMRI_REST1_AP
│ └── HCA6086369_V1_MR_rfMRI_REST1_AP.nii.gz
├── rfMRI_REST1_AP_SBRef
│ └── HCA6086369_V1_MR_rfMRI_REST1_AP_SBRef.nii.gz
├── rfMRI_REST1_PA
│ └── HCA6086369_V1_MR_rfMRI_REST1_PA.nii.gz
├── rfMRI_REST1_PA_SBRef
│ └── HCA6086369_V1_MR_rfMRI_REST1_PA_SBRef.nii.gz
├── rfMRI_REST2_AP
│ └── HCA6086369_V1_MR_rfMRI_REST2_AP.nii.gz
├── rfMRI_REST2_AP_SBRef
│ └── HCA6086369_V1_MR_rfMRI_REST2_AP_SBRef.nii.gz
├── rfMRI_REST2_PA
│ └── HCA6086369_V1_MR_rfMRI_REST2_PA.nii.gz
├── rfMRI_REST2_PA_SBRef
│ └── HCA6086369_V1_MR_rfMRI_REST2_PA_SBRef.nii.gz
├── SpinEchoFieldMap1
│ ├── HCA6086369_V1_MR_SpinEchoFieldMap_AP.nii.gz
│ └── HCA6086369_V1_MR_SpinEchoFieldMap_PA.nii.gz
├── SpinEchoFieldMap2
│ ├── HCA6086369_V1_MR_SpinEchoFieldMap_AP.nii.gz
│ └── HCA6086369_V1_MR_SpinEchoFieldMap_PA.nii.gz
├── SpinEchoFieldMap3
│ ├── HCA6086369_V1_MR_SpinEchoFieldMap_AP.nii.gz
│ └── HCA6086369_V1_MR_SpinEchoFieldMap_PA.nii.gz
├── T1w
│ └── HCA6086369_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz
├── T2w
│ └── HCA6086369_V1_MR_T2w_SPC_vNav.nii.gz
├── tfMRI_CARIT_PA
│ └── HCA6086369_V1_MR_tfMRI_CARIT_PA.nii.gz
├── tfMRI_CARIT_PA_SBRef
│ └── HCA6086369_V1_MR_tfMRI_CARIT_PA_SBRef.nii.gz
├── tfMRI_FACENAME_PA
│ └── HCA6086369_V1_MR_tfMRI_FACENAME_PA.nii.gz
├── tfMRI_FACENAME_PA_SBRef
│ └── HCA6086369_V1_MR_tfMRI_FACENAME_PA_SBRef.nii.gz
├── tfMRI_VISMOTOR_PA
│ └── HCA6086369_V1_MR_tfMRI_VISMOTOR_PA.nii.gz
└── tfMRI_VISMOTOR_PA_SBRef
└── HCA6086369_V1_MR_tfMRI_VISMOTOR_PA_SBRef.nii.gz
As you see your data is not organized in the HCP folder structure. The problem with your data is that QuNex cannot reliably extract additional imaging information that is required for processing from it (e.g. which image is what exactly).
The easiest way from what you have to QuNex onboarding is to organize everything into BIDS and then onboard with import_bids. When doing so, you also need to pay attention to IntendedFor fields in the .json files as they link fieldmaps and spin echos with the imaging data.
Best, Jure
Hi Jure,
Thanks for your reply! I tried to organize the data as the example that you given above:
├── HOH002_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210908151323_9a.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210908151323_9a.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210908151323_9a.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_10a.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_10a.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_10a.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_10a.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_10a.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_12a.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_12a.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_12a.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_13a.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_13a.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_13a.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_14a.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_14a.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_14a.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_15a.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_15a.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_15a.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_17a.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_17a.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210908151323_17a.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210908151323_24a.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210908151323_24a.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210908151323_24a.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210908151323_5a.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210908151323_5a.nii
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210908151323_5a.zip
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210908151323_6a.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210908151323_6a.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20210908151323_6a.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20210908151323_7a.json
│ ├── DICOM_t2_space_cs_sag_20210908151323_7a.nii
│ ├── DICOM_t2_space_cs_sag_20210908151323_7a.zip
│ ├── DICOM_t2_space_cs_sag_20210908151323_8a.json
│ ├── DICOM_t2_space_cs_sag_20210908151323_8a.nii
│ └── DICOM_t2_space_cs_sag_20210908151323_8a.zip
├── HOH003_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210901161019_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210901161019_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210901161019_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_11.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_11.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_11.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_16.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_16.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901161019_16.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210901161019_17.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210901161019_17.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210901161019_17.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210901161019_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210901161019_5.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20210901161019_5.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20210901161019_7.json
│ ├── DICOM_t2_space_cs_sag_20210901161019_7.nii
│ └── DICOM_t2_space_cs_sag_20210901161019_7.zip
├── HOH006_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210901141927_17.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210901141927_17.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210901141927_17.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_18.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_18.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_18.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_18.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_18.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_20.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_20.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_20.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_21.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_21.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_21.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_22.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_22.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_22.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_23.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_23.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_23.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_25.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_25.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210901141927_25.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210901141927_26.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210901141927_26.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210901141927_26.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210901141927_15.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210901141927_15.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20210901141927_15.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20210901141927_13.json
│ ├── DICOM_t2_space_cs_sag_20210901141927_13.nii
│ └── DICOM_t2_space_cs_sag_20210901141927_13.zip
├── HOH011_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210902153845_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210902153845_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210902153845_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_11.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_11.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_11.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_16.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_16.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902153845_16.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210902153845_20.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210902153845_20.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210902153845_20.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210902153845_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210902153845_5.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20210902153845_5.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20210902153845_7.json
│ ├── DICOM_t2_space_cs_sag_20210902153845_7.nii
│ └── DICOM_t2_space_cs_sag_20210902153845_7.zip
├── HOH013_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210902133540_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210902133540_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210902133540_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_11.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_11.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_11.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_16.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_16.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210902133540_16.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210902133540_21.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210902133540_21.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210902133540_21.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210902133540_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210902133540_5.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20210902133540_5.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20210902133540_7.json
│ ├── DICOM_t2_space_cs_sag_20210902133540_7.nii
│ └── DICOM_t2_space_cs_sag_20210902133540_7.zip
├── HOH015_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210917095531_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210917095531_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20210917095531_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_11.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_11.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_11.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_16.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_16.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20210917095531_16.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210917095531_20.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210917095531_20.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20210917095531_20.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210917095531_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210917095531_5.nii
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210917095531_5.zip
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210917095531_6.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20210917095531_6.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20210917095531_6.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20210917095531_7.json
│ ├── DICOM_t2_space_cs_sag_20210917095531_7.nii
│ ├── DICOM_t2_space_cs_sag_20210917095531_7.zip
│ ├── DICOM_t2_space_cs_sag_20210917095531_8.json
│ ├── DICOM_t2_space_cs_sag_20210917095531_8.nii
│ └── DICOM_t2_space_cs_sag_20210917095531_8.zip
├── HOH019_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211117104554_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211117104554_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211117104554_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_15.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_15.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_15.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_17.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_17.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117104554_17.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211117104554_24.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211117104554_24.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211117104554_24.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117104554_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117104554_5.nii
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117104554_5.zip
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117104554_6.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117104554_6.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20211117104554_6.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20211117104554_7.json
│ ├── DICOM_t2_space_cs_sag_20211117104554_7.nii
│ ├── DICOM_t2_space_cs_sag_20211117104554_7.zip
│ ├── DICOM_t2_space_cs_sag_20211117104554_8.json
│ ├── DICOM_t2_space_cs_sag_20211117104554_8.nii
│ └── DICOM_t2_space_cs_sag_20211117104554_8.zip
├── HOH020_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211217090753_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211217090753_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211217090753_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_15.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_15.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_15.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_17.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_17.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211217090753_17.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211217090753_30.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211217090753_30.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211217090753_30.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211217090753_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211217090753_5.nii
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211217090753_5.zip
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211217090753_6.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211217090753_6.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20211217090753_6.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20211217090753_7.json
│ ├── DICOM_t2_space_cs_sag_20211217090753_7.nii
│ ├── DICOM_t2_space_cs_sag_20211217090753_7.zip
│ ├── DICOM_t2_space_cs_sag_20211217090753_8.json
│ ├── DICOM_t2_space_cs_sag_20211217090753_8.nii
│ └── DICOM_t2_space_cs_sag_20211217090753_8.zip
├── HOS005_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211117085825_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211117085825_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211117085825_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_15.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_15.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_15.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_17.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_17.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211117085825_17.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211117085825_24.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211117085825_24.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211117085825_24.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117085825_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117085825_5.nii
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117085825_5.zip
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117085825_6.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211117085825_6.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20211117085825_6.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20211117085825_7.json
│ ├── DICOM_t2_space_cs_sag_20211117085825_7.nii
│ ├── DICOM_t2_space_cs_sag_20211117085825_7.zip
│ ├── DICOM_t2_space_cs_sag_20211117085825_8.json
│ ├── DICOM_t2_space_cs_sag_20211117085825_8.nii
│ └── DICOM_t2_space_cs_sag_20211117085825_8.zip
├── HOS006_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211206145034_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211206145034_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211206145034_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_15.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_15.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_15.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_17.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_17.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206145034_17.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211206145034_18.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211206145034_18.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211206145034_18.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206145034_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206145034_5.nii
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206145034_5.zip
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206145034_6.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206145034_6.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20211206145034_6.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20211206145034_7.json
│ ├── DICOM_t2_space_cs_sag_20211206145034_7.nii
│ ├── DICOM_t2_space_cs_sag_20211206145034_7.zip
│ ├── DICOM_t2_space_cs_sag_20211206145034_8.json
│ ├── DICOM_t2_space_cs_sag_20211206145034_8.nii
│ └── DICOM_t2_space_cs_sag_20211206145034_8.zip
├── HOS007_pre
│ └── unprocessed
│ ├── Diffusion
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211206110948_9.json
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211206110948_9.nii
│ │ ├── DICOM_dti_0_ep2d_mddw_p2s2_64_PA_20211206110948_9.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1001.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1001.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1001.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1002.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1002.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1002.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1003.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1003.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1003.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1004.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1004.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1004.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1007.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1007.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_1007.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_10.bval
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_10.bvec
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_10.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_10.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_10.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_12.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_12.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_12.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_13.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_13.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_13.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_14.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_14.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_14.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_15.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_15.nii
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_15.zip
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_17.json
│ │ ├── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_17.nii
│ │ └── DICOM_dti_ep2d_mddw_p2s2_64_AP_20211206110948_17.zip
│ ├── rfMRI_REST1_AP
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211206110948_18.json
│ │ ├── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211206110948_18.nii
│ │ └── DICOM_rs_fMRI_bold_iso_p2s3_340_Open_Eyes_20211206110948_18.zip
│ ├── T1w
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206110948_5.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206110948_5.nii
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206110948_5.zip
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206110948_6.json
│ │ ├── DICOM_t1_mprage_we_sag_iso_20211206110948_6.nii
│ │ └── DICOM_t1_mprage_we_sag_iso_20211206110948_6.zip
│ └── T2w
│ ├── DICOM_t2_space_cs_sag_20211206110948_7.json
│ ├── DICOM_t2_space_cs_sag_20211206110948_7.nii
│ ├── DICOM_t2_space_cs_sag_20211206110948_7.zip
│ ├── DICOM_t2_space_cs_sag_20211206110948_8.json
│ ├── DICOM_t2_space_cs_sag_20211206110948_8.nii
│ └── DICOM_t2_space_cs_sag_20211206110948_8.zip
However, it still got an error:
subject HOS006, session pre had no images found to be mapped
subject HOS007, session pre had no images found to be mapped
subject HOH011, session pre had no images found to be mapped
subject HOH013, session pre had no images found to be mapped
subject HOS009, session pre had no images found to be mapped
subject HOH015, session pre had no images found to be mapped
subject HOH003, session pre had no images found to be mapped
subject HOH019, session pre had no images found to be mapped
subject HOH006, session pre had no images found to be mapped
subject HOH020, session pre had no images found to be mapped
subject HOH002, session pre had no images found to be mapped
subject HOS005, session pre had no images found to be mapped
Here is my log file:validationdata_import_hcp_2025.07.04-15.09.55.txt (9.2 KB)
Best,
It is not only the organization in folders, but also the names of the files. My example above shows how BOLDs, diffusion, T1w, T2w and SpinEchos need to be named.
I think it would be easier for you to get everything into BIDS format and onboard that way.
Best, Jure
Hi Jure,
Always thanks your kindly help! I have tried both “import_hcp” and “import_bids” but both of them were failed. Can you help me check that my data is named and organized correctly?
My BIDS data are organized as followed:
├── HOH002_pre
│ ├── anat
│ │ ├── HOH002_pre_T1w.json
│ │ ├── HOH002_pre_T1w.nii
│ │ ├── HOH002_pre_T2w.json
│ │ └── HOH002_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH002_pre_ses-1_AP_dwi.bval
│ │ ├── HOH002_pre_ses-1_AP_dwi.bvec
│ │ ├── HOH002_pre_ses-1_AP_dwi.json
│ │ ├── HOH002_pre_ses-1_AP_dwi.nii
│ │ ├── HOH002_pre_ses-1_PA_dwi.json
│ │ └── HOH002_pre_ses-1_PA_dwi.nii
│ └── func
│ ├── HOH002_pre_task-rest_dir-AP.json
│ └── HOH002_pre_task-rest_dir-AP.nii
├── HOH002_pre.zip
├── HOH003_pre
│ ├── anat
│ │ ├── HOH003_pre_T1w.json
│ │ ├── HOH003_pre_T1w.nii
│ │ ├── HOH003_pre_T2w.json
│ │ └── HOH003_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH003_pre_ses-10_AP_dwi.bval
│ │ ├── HOH003_pre_ses-10_AP_dwi.bvec
│ │ ├── HOH003_pre_ses-10_AP_dwi.json
│ │ ├── HOH003_pre_ses-10_AP_dwi.nii
│ │ ├── HOH003_pre_ses-11_AP_dwi.json
│ │ ├── HOH003_pre_ses-11_AP_dwi.nii
│ │ ├── HOH003_pre_ses-12_AP_dwi.json
│ │ ├── HOH003_pre_ses-12_AP_dwi.nii
│ │ ├── HOH003_pre_ses-13_AP_dwi.json
│ │ ├── HOH003_pre_ses-13_AP_dwi.nii
│ │ ├── HOH003_pre_ses-14_AP_dwi.json
│ │ ├── HOH003_pre_ses-14_AP_dwi.nii
│ │ ├── HOH003_pre_ses-16_AP_dwi.json
│ │ ├── HOH003_pre_ses-16_AP_dwi.nii
│ │ ├── HOH003_pre_ses-9_PA_dwi.json
│ │ └── HOH003_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOH003_pre_task-rest_dir-AP.json
│ └── HOH003_pre_task-rest_dir-AP.nii
├── HOH003_pre.zip
├── HOH006_pre
│ ├── anat
│ │ ├── HOH006_pre_T1w.json
│ │ ├── HOH006_pre_T1w.nii
│ │ ├── HOH006_pre_T2w.json
│ │ └── HOH006_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH006_pre_ses-17_PA_dwi.json
│ │ ├── HOH006_pre_ses-17_PA_dwi.nii
│ │ ├── HOH006_pre_ses-18_AP_dwi.bval
│ │ ├── HOH006_pre_ses-18_AP_dwi.bvec
│ │ ├── HOH006_pre_ses-18_AP_dwi.json
│ │ ├── HOH006_pre_ses-18_AP_dwi.nii
│ │ ├── HOH006_pre_ses-20_AP_dwi.json
│ │ ├── HOH006_pre_ses-20_AP_dwi.nii
│ │ ├── HOH006_pre_ses-21_AP_dwi.json
│ │ ├── HOH006_pre_ses-21_AP_dwi.nii
│ │ ├── HOH006_pre_ses-22_AP_dwi.json
│ │ ├── HOH006_pre_ses-22_AP_dwi.nii
│ │ ├── HOH006_pre_ses-23_AP_dwi.json
│ │ ├── HOH006_pre_ses-23_AP_dwi.nii
│ │ ├── HOH006_pre_ses-25_AP_dwi.json
│ │ └── HOH006_pre_ses-25_AP_dwi.nii
│ └── func
│ ├── HOH006_pre_task-rest_dir-AP.json
│ └── HOH006_pre_task-rest_dir-AP.nii
├── HOH006_pre.zip
├── HOH011_pre
│ ├── anat
│ │ ├── HOH011_pre_T1w.json
│ │ ├── HOH011_pre_T1w.nii
│ │ ├── HOH011_pre_T2w.json
│ │ └── HOH011_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH011_pre_ses-10_AP_dwi.bval
│ │ ├── HOH011_pre_ses-10_AP_dwi.bvec
│ │ ├── HOH011_pre_ses-10_AP_dwi.json
│ │ ├── HOH011_pre_ses-10_AP_dwi.nii
│ │ ├── HOH011_pre_ses-11_AP_dwi.json
│ │ ├── HOH011_pre_ses-11_AP_dwi.nii
│ │ ├── HOH011_pre_ses-12_AP_dwi.json
│ │ ├── HOH011_pre_ses-12_AP_dwi.nii
│ │ ├── HOH011_pre_ses-13_AP_dwi.json
│ │ ├── HOH011_pre_ses-13_AP_dwi.nii
│ │ ├── HOH011_pre_ses-14_AP_dwi.json
│ │ ├── HOH011_pre_ses-14_AP_dwi.nii
│ │ ├── HOH011_pre_ses-16_AP_dwi.json
│ │ ├── HOH011_pre_ses-16_AP_dwi.nii
│ │ ├── HOH011_pre_ses-9_PA_dwi.json
│ │ └── HOH011_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOH011_pre_task-rest_dir-AP.json
│ └── HOH011_pre_task-rest_dir-AP.nii
├── HOH011_pre.zip
├── HOH013_pre
│ ├── anat
│ │ ├── HOH013_pre_T1w.json
│ │ ├── HOH013_pre_T1w.nii
│ │ ├── HOH013_pre_T2w.json
│ │ └── HOH013_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH013_pre_ses-10_AP_dwi.bval
│ │ ├── HOH013_pre_ses-10_AP_dwi.bvec
│ │ ├── HOH013_pre_ses-10_AP_dwi.json
│ │ ├── HOH013_pre_ses-10_AP_dwi.nii
│ │ ├── HOH013_pre_ses-11_AP_dwi.json
│ │ ├── HOH013_pre_ses-11_AP_dwi.nii
│ │ ├── HOH013_pre_ses-12_AP_dwi.json
│ │ ├── HOH013_pre_ses-12_AP_dwi.nii
│ │ ├── HOH013_pre_ses-13_AP_dwi.json
│ │ ├── HOH013_pre_ses-13_AP_dwi.nii
│ │ ├── HOH013_pre_ses-14_AP_dwi.json
│ │ ├── HOH013_pre_ses-14_AP_dwi.nii
│ │ ├── HOH013_pre_ses-16_AP_dwi.json
│ │ ├── HOH013_pre_ses-16_AP_dwi.nii
│ │ ├── HOH013_pre_ses-9_PA_dwi.json
│ │ └── HOH013_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOH013_pre_task-rest_dir-AP.json
│ └── HOH013_pre_task-rest_dir-AP.nii
├── HOH013_pre.zip
├── HOH015_pre
│ ├── anat
│ │ ├── HOH015_pre_T1w.json
│ │ ├── HOH015_pre_T1w.nii
│ │ ├── HOH015_pre_T2w.json
│ │ └── HOH015_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH015_pre_ses-10_AP_dwi.bval
│ │ ├── HOH015_pre_ses-10_AP_dwi.bvec
│ │ ├── HOH015_pre_ses-10_AP_dwi.json
│ │ ├── HOH015_pre_ses-10_AP_dwi.nii
│ │ ├── HOH015_pre_ses-11_AP_dwi.json
│ │ ├── HOH015_pre_ses-11_AP_dwi.nii
│ │ ├── HOH015_pre_ses-12_AP_dwi.json
│ │ ├── HOH015_pre_ses-12_AP_dwi.nii
│ │ ├── HOH015_pre_ses-13_AP_dwi.json
│ │ ├── HOH015_pre_ses-13_AP_dwi.nii
│ │ ├── HOH015_pre_ses-14_AP_dwi.json
│ │ ├── HOH015_pre_ses-14_AP_dwi.nii
│ │ ├── HOH015_pre_ses-16_AP_dwi.json
│ │ ├── HOH015_pre_ses-16_AP_dwi.nii
│ │ ├── HOH015_pre_ses-9_PA_dwi.json
│ │ └── HOH015_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOH015_pre_task-rest_dir-AP.json
│ └── HOH015_pre_task-rest_dir-AP.nii
├── HOH015_pre.zip
├── HOH019_pre
│ ├── anat
│ │ ├── HOH019_pre_T1w.json
│ │ ├── HOH019_pre_T1w.nii
│ │ ├── HOH019_pre_T2w.json
│ │ └── HOH019_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH019_pre_ses-10_AP_dwi.bval
│ │ ├── HOH019_pre_ses-10_AP_dwi.bvec
│ │ ├── HOH019_pre_ses-10_AP_dwi.json
│ │ ├── HOH019_pre_ses-10_AP_dwi.nii
│ │ ├── HOH019_pre_ses-12_AP_dwi.json
│ │ ├── HOH019_pre_ses-12_AP_dwi.nii
│ │ ├── HOH019_pre_ses-13_AP_dwi.json
│ │ ├── HOH019_pre_ses-13_AP_dwi.nii
│ │ ├── HOH019_pre_ses-14_AP_dwi.json
│ │ ├── HOH019_pre_ses-14_AP_dwi.nii
│ │ ├── HOH019_pre_ses-15_AP_dwi.json
│ │ ├── HOH019_pre_ses-15_AP_dwi.nii
│ │ ├── HOH019_pre_ses-17_AP_dwi.json
│ │ ├── HOH019_pre_ses-17_AP_dwi.nii
│ │ ├── HOH019_pre_ses-9_PA_dwi.json
│ │ └── HOH019_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOH019_pre_task-rest_dir-AP.json
│ └── HOH019_pre_task-rest_dir-AP.nii
├── HOH019_pre.zip
├── HOH020_pre
│ ├── anat
│ │ ├── HOH020_pre_T1w.json
│ │ ├── HOH020_pre_T1w.nii
│ │ ├── HOH020_pre_T2w.json
│ │ └── HOH020_pre_T2w.nii
│ ├── dwi
│ │ ├── HOH020_pre_ses-10_AP_dwi.bval
│ │ ├── HOH020_pre_ses-10_AP_dwi.bvec
│ │ ├── HOH020_pre_ses-10_AP_dwi.json
│ │ ├── HOH020_pre_ses-10_AP_dwi.nii
│ │ ├── HOH020_pre_ses-12_AP_dwi.json
│ │ ├── HOH020_pre_ses-12_AP_dwi.nii
│ │ ├── HOH020_pre_ses-13_AP_dwi.json
│ │ ├── HOH020_pre_ses-13_AP_dwi.nii
│ │ ├── HOH020_pre_ses-14_AP_dwi.json
│ │ ├── HOH020_pre_ses-14_AP_dwi.nii
│ │ ├── HOH020_pre_ses-15_AP_dwi.json
│ │ ├── HOH020_pre_ses-15_AP_dwi.nii
│ │ ├── HOH020_pre_ses-17_AP_dwi.json
│ │ ├── HOH020_pre_ses-17_AP_dwi.nii
│ │ ├── HOH020_pre_ses-9_PA_dwi.json
│ │ └── HOH020_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOH020_pre_task-rest_dir-AP.json
│ └── HOH020_pre_task-rest_dir-AP.nii
├── HOH020_pre.zip
├── HOS005_pre
│ ├── anat
│ │ ├── HOS005_pre_T1w.json
│ │ ├── HOS005_pre_T1w.nii
│ │ ├── HOS005_pre_T2w.json
│ │ └── HOS005_pre_T2w.nii
│ ├── dwi
│ │ ├── HOS005_pre_ses-10_AP_dwi.bval
│ │ ├── HOS005_pre_ses-10_AP_dwi.bvec
│ │ ├── HOS005_pre_ses-10_AP_dwi.json
│ │ ├── HOS005_pre_ses-10_AP_dwi.nii
│ │ ├── HOS005_pre_ses-12_AP_dwi.json
│ │ ├── HOS005_pre_ses-12_AP_dwi.nii
│ │ ├── HOS005_pre_ses-13_AP_dwi.json
│ │ ├── HOS005_pre_ses-13_AP_dwi.nii
│ │ ├── HOS005_pre_ses-14_AP_dwi.json
│ │ ├── HOS005_pre_ses-14_AP_dwi.nii
│ │ ├── HOS005_pre_ses-15_AP_dwi.json
│ │ ├── HOS005_pre_ses-15_AP_dwi.nii
│ │ ├── HOS005_pre_ses-17_AP_dwi.json
│ │ ├── HOS005_pre_ses-17_AP_dwi.nii
│ │ ├── HOS005_pre_ses-9_PA_dwi.json
│ │ └── HOS005_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOS005_pre_task-rest_dir-AP.json
│ └── HOS005_pre_task-rest_dir-AP.nii
├── HOS005_pre.zip
├── HOS006_pre
│ ├── anat
│ │ ├── HOS006_pre_T1w.json
│ │ ├── HOS006_pre_T1w.nii
│ │ ├── HOS006_pre_T2w.json
│ │ └── HOS006_pre_T2w.nii
│ ├── dwi
│ │ ├── HOS006_pre_ses-10_AP_dwi.bval
│ │ ├── HOS006_pre_ses-10_AP_dwi.bvec
│ │ ├── HOS006_pre_ses-10_AP_dwi.json
│ │ ├── HOS006_pre_ses-10_AP_dwi.nii
│ │ ├── HOS006_pre_ses-12_AP_dwi.json
│ │ ├── HOS006_pre_ses-12_AP_dwi.nii
│ │ ├── HOS006_pre_ses-13_AP_dwi.json
│ │ ├── HOS006_pre_ses-13_AP_dwi.nii
│ │ ├── HOS006_pre_ses-14_AP_dwi.json
│ │ ├── HOS006_pre_ses-14_AP_dwi.nii
│ │ ├── HOS006_pre_ses-15_AP_dwi.json
│ │ ├── HOS006_pre_ses-15_AP_dwi.nii
│ │ ├── HOS006_pre_ses-17_AP_dwi.json
│ │ ├── HOS006_pre_ses-17_AP_dwi.nii
│ │ ├── HOS006_pre_ses-9_PA_dwi.json
│ │ └── HOS006_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOS006_pre_task-rest_dir-AP.json
│ └── HOS006_pre_task-rest_dir-AP.nii
├── HOS006_pre.zip
├── HOS007_pre
│ ├── anat
│ │ ├── HOS007_pre_T1w.json
│ │ ├── HOS007_pre_T1w.nii
│ │ ├── HOS007_pre_T2w.json
│ │ └── HOS007_pre_T2w.nii
│ ├── dwi
│ │ ├── HOS007_pre_ses-1001_AP_dwi.json
│ │ ├── HOS007_pre_ses-1001_AP_dwi.nii
│ │ ├── HOS007_pre_ses-1002_AP_dwi.json
│ │ ├── HOS007_pre_ses-1002_AP_dwi.nii
│ │ ├── HOS007_pre_ses-1003_AP_dwi.json
│ │ ├── HOS007_pre_ses-1003_AP_dwi.nii
│ │ ├── HOS007_pre_ses-1004_AP_dwi.json
│ │ ├── HOS007_pre_ses-1004_AP_dwi.nii
│ │ ├── HOS007_pre_ses-1007_AP_dwi.json
│ │ ├── HOS007_pre_ses-1007_AP_dwi.nii
│ │ ├── HOS007_pre_ses-10_AP_dwi.bval
│ │ ├── HOS007_pre_ses-10_AP_dwi.bvec
│ │ ├── HOS007_pre_ses-10_AP_dwi.json
│ │ ├── HOS007_pre_ses-10_AP_dwi.nii
│ │ ├── HOS007_pre_ses-12_AP_dwi.json
│ │ ├── HOS007_pre_ses-12_AP_dwi.nii
│ │ ├── HOS007_pre_ses-13_AP_dwi.json
│ │ ├── HOS007_pre_ses-13_AP_dwi.nii
│ │ ├── HOS007_pre_ses-14_AP_dwi.json
│ │ ├── HOS007_pre_ses-14_AP_dwi.nii
│ │ ├── HOS007_pre_ses-15_AP_dwi.json
│ │ ├── HOS007_pre_ses-15_AP_dwi.nii
│ │ ├── HOS007_pre_ses-17_AP_dwi.json
│ │ ├── HOS007_pre_ses-17_AP_dwi.nii
│ │ ├── HOS007_pre_ses-9_PA_dwi.json
│ │ └── HOS007_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOS007_pre_task-rest_dir-AP.json
│ └── HOS007_pre_task-rest_dir-AP.nii
├── HOS007_pre.zip
├── HOS009_pre
│ ├── anat
│ │ ├── HOS009_pre_T1w.json
│ │ ├── HOS009_pre_T1w.nii
│ │ ├── HOS009_pre_T2w.json
│ │ └── HOS009_pre_T2w.nii
│ ├── dwi
│ │ ├── HOS009_pre_ses-10_AP_dwi.bval
│ │ ├── HOS009_pre_ses-10_AP_dwi.bvec
│ │ ├── HOS009_pre_ses-10_AP_dwi.json
│ │ ├── HOS009_pre_ses-10_AP_dwi.nii
│ │ ├── HOS009_pre_ses-12_AP_dwi.json
│ │ ├── HOS009_pre_ses-12_AP_dwi.nii
│ │ ├── HOS009_pre_ses-13_AP_dwi.json
│ │ ├── HOS009_pre_ses-13_AP_dwi.nii
│ │ ├── HOS009_pre_ses-14_AP_dwi.json
│ │ ├── HOS009_pre_ses-14_AP_dwi.nii
│ │ ├── HOS009_pre_ses-15_AP_dwi.json
│ │ ├── HOS009_pre_ses-15_AP_dwi.nii
│ │ ├── HOS009_pre_ses-17_AP_dwi.json
│ │ ├── HOS009_pre_ses-17_AP_dwi.nii
│ │ ├── HOS009_pre_ses-9_PA_dwi.json
│ │ └── HOS009_pre_ses-9_PA_dwi.nii
│ └── func
│ ├── HOS009_pre_task-rest_dir-AP.json
│ └── HOS009_pre_task-rest_dir-AP.nii
└── HOS009_pre.zip
And my HCP data are organized as followed:
├── HOH002
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH002_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH002_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH002_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH002_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH002_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH002_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH002_rfMRI_REST1_AP.json
│ │ └── HOH002_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH002_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH002_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH002_T2w_SPC_vNav.json
│ └── HOH002_T2w_SPC_vNav.nii.gz
├── HOH002.zip
├── HOH003
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH003_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH003_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH003_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH003_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH003_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH003_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH003_rfMRI_REST1_AP.json
│ │ └── HOH003_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH003_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH003_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH003_T2w_SPC_vNav.json
│ └── HOH003_T2w_SPC_vNav.nii.gz
├── HOH003.zip
├── HOH006
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH006_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH006_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH006_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH006_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH006_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH006_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH006_rfMRI_REST1_AP.json
│ │ └── HOH006_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH006_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH006_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH006_T2w_SPC_vNav.json
│ └── HOH006_T2w_SPC_vNav.nii.gz
├── HOH006.zip
├── HOH011
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH011_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH011_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH011_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH011_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH011_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH011_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH011_rfMRI_REST1_AP.json
│ │ └── HOH011_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH011_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH011_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH011_T2w_SPC_vNav.json
│ └── HOH011_T2w_SPC_vNav.nii.gz
├── HOH011.zip
├── HOH013
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH013_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH013_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH013_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH013_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH013_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH013_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH013_rfMRI_REST1_AP.json
│ │ └── HOH013_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH013_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH013_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH013_T2w_SPC_vNav.json
│ └── HOH013_T2w_SPC_vNav.nii.gz
├── HOH013.zip
├── HOH015
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH015_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH015_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH015_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH015_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH015_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH015_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH015_rfMRI_REST1_AP.json
│ │ └── HOH015_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH015_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH015_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH015_T2w_SPC_vNav.json
│ └── HOH015_T2w_SPC_vNav.nii.gz
├── HOH015.zip
├── HOH019
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH019_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH019_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH019_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH019_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH019_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH019_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH019_rfMRI_REST1_AP.json
│ │ └── HOH019_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH019_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH019_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH019_T2w_SPC_vNav.json
│ └── HOH019_T2w_SPC_vNav.nii.gz
├── HOH019.zip
├── HOH020
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOH020_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOH020_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOH020_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOH020_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOH020_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOH020_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOH020_rfMRI_REST1_AP.json
│ │ └── HOH020_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOH020_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOH020_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOH020_T2w_SPC_vNav.json
│ └── HOH020_T2w_SPC_vNav.nii.gz
├── HOH020.zip
├── HOS005
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOS005_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOS005_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOS005_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOS005_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOS005_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOS005_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOS005_rfMRI_REST1_AP.json
│ │ └── HOS005_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOS005_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOS005_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOS005_T2w_SPC_vNav.json
│ └── HOS005_T2w_SPC_vNav.nii.gz
├── HOS005.zip
├── HOS006
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOS006_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOS006_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOS006_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOS006_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOS006_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOS006_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOS006_rfMRI_REST1_AP.json
│ │ └── HOS006_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOS006_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOS006_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOS006_T2w_SPC_vNav.json
│ └── HOS006_T2w_SPC_vNav.nii.gz
├── HOS006.zip
├── HOS007
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOS007_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOS007_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOS007_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOS007_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOS007_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOS007_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOS007_rfMRI_REST1_AP.json
│ │ └── HOS007_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOS007_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOS007_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOS007_T2w_SPC_vNav.json
│ └── HOS007_T2w_SPC_vNav.nii.gz
├── HOS007.zip
├── HOS009
│ └── unprocessed
│ ├── Diffusion
│ │ ├── HOS009_dMRI_dir64_AP_dir64_AP.bval
│ │ ├── HOS009_dMRI_dir64_AP_dir64_AP.bvec
│ │ ├── HOS009_dMRI_dir64_AP_dir64_AP.json
│ │ ├── HOS009_dMRI_dir64_AP_dir64_AP.nii.gz
│ │ ├── HOS009_dMRI_dir64_PA_dir64_PA.json
│ │ └── HOS009_dMRI_dir64_PA_dir64_PA.nii.gz
│ ├── rfMRI_REST1_AP
│ │ ├── HOS009_rfMRI_REST1_AP.json
│ │ └── HOS009_rfMRI_REST1_AP.nii.gz
│ ├── T1w
│ │ ├── HOS009_T1w_MPR_vNav_4e_RMS.json
│ │ └── HOS009_T1w_MPR_vNav_4e_RMS.nii.gz
│ └── T2w
│ ├── HOS009_T2w_SPC_vNav.json
│ └── HOS009_T2w_SPC_vNav.nii.gz
└── HOS009.zip
Best,
Let’s focus on the BIDS version, so we are not resolving multiple issues at the same time. At a glance it looks good (note that I am not a BIDS expert though import_bids command that you used and the error log?
One thing I would to is to move the .zip files to a different folder. QuNex can onboard from folders or from zip archives and this might give you doube imports or cause some issues.
Best, Jure
yzhong
July 5, 2025, 12:01pm
8
Sure, my command is:
qunex_container import_bids \
--sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
--sessions="${SUBJ}" \
--inbox="${RAW_DATA}" \
--archive="leave" \
--bind="/hdd1:/hdd1" \
--container="${QUNEX_CONTAINER}" \
--overwrite="yes"
And here is the log file:validation2_import_bids_2025.07.05-18.57.50.txt (8.5 KB)
There is an issue with one of the JSON files. Based on the log I would say for session HOS009_pre. Hard to say which one exactly, but it seems like there is an invalid character in one of them:
Invalid control character at: line 17 column 32 (char 610)
Since you have 12 sessions, you can onboard 1 by 1 by running the command and setting --session for each one of them. Based on the log it worked for all of them except HOS009_pre.
And like I said it is probably not good practice to have zipped and unzipped BIDS data in the same root folder and then import from there.
Best, Jure
yzhong
July 6, 2025, 7:56am
10
Hi Jure,
I have tried to only keep .zip files in my data path, but the error is the same. And I also checked my session file, it seems like only dwi files imported sucessfully even though the name are wired:
├── 1
│ └── bids
│ └── dwi
│ ├── HOH002_pre_ses-1_AP_dwi.bval
│ ├── HOH002_pre_ses-1_AP_dwi.bvec
│ ├── HOH002_pre_ses-1_AP_dwi.json
│ ├── HOH002_pre_ses-1_AP_dwi.nii.gz
│ ├── HOH002_pre_ses-1_PA_dwi.json
│ └── HOH002_pre_ses-1_PA_dwi.nii.gz
├── 10
│ └── bids
│ └── dwi
│ ├── HOH003_pre_ses-10_AP_dwi.bval
│ ├── HOH003_pre_ses-10_AP_dwi.bvec
│ ├── HOH003_pre_ses-10_AP_dwi.json
│ ├── HOH003_pre_ses-10_AP_dwi.nii.gz
│ ├── HOH011_pre_ses-10_AP_dwi.bval
│ ├── HOH011_pre_ses-10_AP_dwi.bvec
│ ├── HOH011_pre_ses-10_AP_dwi.json
│ ├── HOH011_pre_ses-10_AP_dwi.nii.gz
│ ├── HOH013_pre_ses-10_AP_dwi.bval
│ ├── HOH013_pre_ses-10_AP_dwi.bvec
│ ├── HOH013_pre_ses-10_AP_dwi.json
│ ├── HOH013_pre_ses-10_AP_dwi.nii.gz
│ ├── HOH015_pre_ses-10_AP_dwi.bval
│ ├── HOH015_pre_ses-10_AP_dwi.bvec
│ ├── HOH015_pre_ses-10_AP_dwi.json
│ ├── HOH015_pre_ses-10_AP_dwi.nii.gz
│ ├── HOH019_pre_ses-10_AP_dwi.bval
│ ├── HOH019_pre_ses-10_AP_dwi.bvec
│ ├── HOH019_pre_ses-10_AP_dwi.json
│ ├── HOH019_pre_ses-10_AP_dwi.nii.gz
│ ├── HOH020_pre_ses-10_AP_dwi.bval
│ ├── HOH020_pre_ses-10_AP_dwi.bvec
│ ├── HOH020_pre_ses-10_AP_dwi.json
│ ├── HOH020_pre_ses-10_AP_dwi.nii.gz
│ ├── HOS005_pre_ses-10_AP_dwi.bval
│ ├── HOS005_pre_ses-10_AP_dwi.bvec
│ ├── HOS005_pre_ses-10_AP_dwi.json
│ ├── HOS005_pre_ses-10_AP_dwi.nii.gz
│ ├── HOS006_pre_ses-10_AP_dwi.bval
│ ├── HOS006_pre_ses-10_AP_dwi.bvec
│ ├── HOS006_pre_ses-10_AP_dwi.json
│ ├── HOS006_pre_ses-10_AP_dwi.nii.gz
│ ├── HOS007_pre_ses-10_AP_dwi.bval
│ ├── HOS007_pre_ses-10_AP_dwi.bvec
│ ├── HOS007_pre_ses-10_AP_dwi.json
│ ├── HOS007_pre_ses-10_AP_dwi.nii.gz
│ ├── HOS009_pre_ses-10_AP_dwi.bval
│ ├── HOS009_pre_ses-10_AP_dwi.bvec
│ ├── HOS009_pre_ses-10_AP_dwi.json
│ └── HOS009_pre_ses-10_AP_dwi.nii.gz
├── 1001
│ └── bids
│ └── dwi
│ ├── HOS007_pre_ses-1001_AP_dwi.json
│ └── HOS007_pre_ses-1001_AP_dwi.nii.gz
├── 1002
│ └── bids
│ └── dwi
│ ├── HOS007_pre_ses-1002_AP_dwi.json
│ └── HOS007_pre_ses-1002_AP_dwi.nii.gz
├── 1003
│ └── bids
│ └── dwi
│ ├── HOS007_pre_ses-1003_AP_dwi.json
│ └── HOS007_pre_ses-1003_AP_dwi.nii.gz
├── 1004
│ └── bids
│ └── dwi
│ ├── HOS007_pre_ses-1004_AP_dwi.json
│ └── HOS007_pre_ses-1004_AP_dwi.nii.gz
├── 1007
│ └── bids
│ └── dwi
│ ├── HOS007_pre_ses-1007_AP_dwi.json
│ └── HOS007_pre_ses-1007_AP_dwi.nii.gz
├── 11
│ └── bids
│ └── dwi
│ ├── HOH003_pre_ses-11_AP_dwi.json
│ ├── HOH003_pre_ses-11_AP_dwi.nii.gz
│ ├── HOH011_pre_ses-11_AP_dwi.json
│ ├── HOH011_pre_ses-11_AP_dwi.nii.gz
│ ├── HOH013_pre_ses-11_AP_dwi.json
│ ├── HOH013_pre_ses-11_AP_dwi.nii.gz
│ ├── HOH015_pre_ses-11_AP_dwi.json
│ └── HOH015_pre_ses-11_AP_dwi.nii.gz
├── 12
│ └── bids
│ └── dwi
│ ├── HOH003_pre_ses-12_AP_dwi.json
│ ├── HOH003_pre_ses-12_AP_dwi.nii.gz
│ ├── HOH011_pre_ses-12_AP_dwi.json
│ ├── HOH011_pre_ses-12_AP_dwi.nii.gz
│ ├── HOH013_pre_ses-12_AP_dwi.json
│ ├── HOH013_pre_ses-12_AP_dwi.nii.gz
│ ├── HOH015_pre_ses-12_AP_dwi.json
│ ├── HOH015_pre_ses-12_AP_dwi.nii.gz
│ ├── HOH019_pre_ses-12_AP_dwi.json
│ ├── HOH019_pre_ses-12_AP_dwi.nii.gz
│ ├── HOH020_pre_ses-12_AP_dwi.json
│ ├── HOH020_pre_ses-12_AP_dwi.nii.gz
│ ├── HOS005_pre_ses-12_AP_dwi.json
│ ├── HOS005_pre_ses-12_AP_dwi.nii.gz
│ ├── HOS006_pre_ses-12_AP_dwi.json
│ ├── HOS006_pre_ses-12_AP_dwi.nii.gz
│ ├── HOS007_pre_ses-12_AP_dwi.json
│ ├── HOS007_pre_ses-12_AP_dwi.nii.gz
│ ├── HOS009_pre_ses-12_AP_dwi.json
│ └── HOS009_pre_ses-12_AP_dwi.nii.gz
├── 13
│ └── bids
│ └── dwi
│ ├── HOH003_pre_ses-13_AP_dwi.json
│ ├── HOH003_pre_ses-13_AP_dwi.nii.gz
│ ├── HOH011_pre_ses-13_AP_dwi.json
│ ├── HOH011_pre_ses-13_AP_dwi.nii.gz
│ ├── HOH013_pre_ses-13_AP_dwi.json
│ ├── HOH013_pre_ses-13_AP_dwi.nii.gz
│ ├── HOH015_pre_ses-13_AP_dwi.json
│ ├── HOH015_pre_ses-13_AP_dwi.nii.gz
│ ├── HOH019_pre_ses-13_AP_dwi.json
│ ├── HOH019_pre_ses-13_AP_dwi.nii.gz
│ ├── HOH020_pre_ses-13_AP_dwi.json
│ ├── HOH020_pre_ses-13_AP_dwi.nii.gz
│ ├── HOS005_pre_ses-13_AP_dwi.json
│ ├── HOS005_pre_ses-13_AP_dwi.nii.gz
│ ├── HOS006_pre_ses-13_AP_dwi.json
│ ├── HOS006_pre_ses-13_AP_dwi.nii.gz
│ ├── HOS007_pre_ses-13_AP_dwi.json
│ ├── HOS007_pre_ses-13_AP_dwi.nii.gz
│ ├── HOS009_pre_ses-13_AP_dwi.json
│ └── HOS009_pre_ses-13_AP_dwi.nii.gz
├── 14
│ └── bids
│ └── dwi
│ ├── HOH003_pre_ses-14_AP_dwi.json
│ ├── HOH003_pre_ses-14_AP_dwi.nii.gz
│ ├── HOH011_pre_ses-14_AP_dwi.json
│ ├── HOH011_pre_ses-14_AP_dwi.nii.gz
│ ├── HOH013_pre_ses-14_AP_dwi.json
│ ├── HOH013_pre_ses-14_AP_dwi.nii.gz
│ ├── HOH015_pre_ses-14_AP_dwi.json
│ ├── HOH015_pre_ses-14_AP_dwi.nii.gz
│ ├── HOH019_pre_ses-14_AP_dwi.json
│ ├── HOH019_pre_ses-14_AP_dwi.nii.gz
│ ├── HOH020_pre_ses-14_AP_dwi.json
│ ├── HOH020_pre_ses-14_AP_dwi.nii.gz
│ ├── HOS005_pre_ses-14_AP_dwi.json
│ ├── HOS005_pre_ses-14_AP_dwi.nii.gz
│ ├── HOS006_pre_ses-14_AP_dwi.json
│ ├── HOS006_pre_ses-14_AP_dwi.nii.gz
│ ├── HOS007_pre_ses-14_AP_dwi.json
│ ├── HOS007_pre_ses-14_AP_dwi.nii.gz
│ ├── HOS009_pre_ses-14_AP_dwi.json
│ └── HOS009_pre_ses-14_AP_dwi.nii.gz
├── 15
│ └── bids
│ └── dwi
│ ├── HOH019_pre_ses-15_AP_dwi.json
│ ├── HOH019_pre_ses-15_AP_dwi.nii.gz
│ ├── HOH020_pre_ses-15_AP_dwi.json
│ ├── HOH020_pre_ses-15_AP_dwi.nii.gz
│ ├── HOS005_pre_ses-15_AP_dwi.json
│ ├── HOS005_pre_ses-15_AP_dwi.nii.gz
│ ├── HOS006_pre_ses-15_AP_dwi.json
│ ├── HOS006_pre_ses-15_AP_dwi.nii.gz
│ ├── HOS007_pre_ses-15_AP_dwi.json
│ ├── HOS007_pre_ses-15_AP_dwi.nii.gz
│ ├── HOS009_pre_ses-15_AP_dwi.json
│ └── HOS009_pre_ses-15_AP_dwi.nii.gz
├── 16
│ └── bids
│ └── dwi
│ ├── HOH003_pre_ses-16_AP_dwi.json
│ ├── HOH003_pre_ses-16_AP_dwi.nii.gz
│ ├── HOH011_pre_ses-16_AP_dwi.json
│ ├── HOH011_pre_ses-16_AP_dwi.nii.gz
│ ├── HOH013_pre_ses-16_AP_dwi.json
│ ├── HOH013_pre_ses-16_AP_dwi.nii.gz
│ ├── HOH015_pre_ses-16_AP_dwi.json
│ └── HOH015_pre_ses-16_AP_dwi.nii.gz
├── 17
│ └── bids
│ └── dwi
│ ├── HOH006_pre_ses-17_PA_dwi.json
│ ├── HOH006_pre_ses-17_PA_dwi.nii.gz
│ ├── HOH019_pre_ses-17_AP_dwi.json
│ ├── HOH019_pre_ses-17_AP_dwi.nii.gz
│ ├── HOH020_pre_ses-17_AP_dwi.json
│ ├── HOH020_pre_ses-17_AP_dwi.nii.gz
│ ├── HOS005_pre_ses-17_AP_dwi.json
│ ├── HOS005_pre_ses-17_AP_dwi.nii.gz
│ ├── HOS006_pre_ses-17_AP_dwi.json
│ ├── HOS006_pre_ses-17_AP_dwi.nii.gz
│ ├── HOS007_pre_ses-17_AP_dwi.json
│ ├── HOS007_pre_ses-17_AP_dwi.nii.gz
│ ├── HOS009_pre_ses-17_AP_dwi.json
│ └── HOS009_pre_ses-17_AP_dwi.nii.gz
├── 18
│ └── bids
│ └── dwi
│ ├── HOH006_pre_ses-18_AP_dwi.bval
│ ├── HOH006_pre_ses-18_AP_dwi.bvec
│ ├── HOH006_pre_ses-18_AP_dwi.json
│ └── HOH006_pre_ses-18_AP_dwi.nii.gz
├── 20
│ └── bids
│ └── dwi
│ ├── HOH006_pre_ses-20_AP_dwi.json
│ └── HOH006_pre_ses-20_AP_dwi.nii.gz
├── 21
│ └── bids
│ └── dwi
│ ├── HOH006_pre_ses-21_AP_dwi.json
│ └── HOH006_pre_ses-21_AP_dwi.nii.gz
├── 22
│ └── bids
│ └── dwi
│ ├── HOH006_pre_ses-22_AP_dwi.json
│ └── HOH006_pre_ses-22_AP_dwi.nii.gz
├── 23
│ └── bids
│ └── dwi
│ ├── HOH006_pre_ses-23_AP_dwi.json
│ └── HOH006_pre_ses-23_AP_dwi.nii.gz
├── 25
│ └── bids
│ └── dwi
│ ├── HOH006_pre_ses-25_AP_dwi.json
│ └── HOH006_pre_ses-25_AP_dwi.nii.gz
├── 9
│ └── bids
│ └── dwi
│ ├── HOH003_pre_ses-9_PA_dwi.json
│ ├── HOH003_pre_ses-9_PA_dwi.nii.gz
│ ├── HOH011_pre_ses-9_PA_dwi.json
│ ├── HOH011_pre_ses-9_PA_dwi.nii.gz
│ ├── HOH013_pre_ses-9_PA_dwi.json
│ ├── HOH013_pre_ses-9_PA_dwi.nii.gz
│ ├── HOH015_pre_ses-9_PA_dwi.json
│ ├── HOH015_pre_ses-9_PA_dwi.nii.gz
│ ├── HOH019_pre_ses-9_PA_dwi.json
│ ├── HOH019_pre_ses-9_PA_dwi.nii.gz
│ ├── HOH020_pre_ses-9_PA_dwi.json
│ ├── HOH020_pre_ses-9_PA_dwi.nii.gz
│ ├── HOS005_pre_ses-9_PA_dwi.json
│ ├── HOS005_pre_ses-9_PA_dwi.nii.gz
│ ├── HOS006_pre_ses-9_PA_dwi.json
│ ├── HOS006_pre_ses-9_PA_dwi.nii.gz
│ ├── HOS007_pre_ses-9_PA_dwi.json
│ ├── HOS007_pre_ses-9_PA_dwi.nii.gz
│ ├── HOS009_pre_ses-9_PA_dwi.json
│ └── HOS009_pre_ses-9_PA_dwi.nii.gz
├── archive
│ ├── behavior
│ ├── BIDS
│ ├── EEG
│ ├── HCPLS
│ └── MR
├── inbox
│ ├── behavior
│ ├── BIDS
│ ├── concs
│ ├── EEG
│ ├── events
│ ├── HCPLS
│ └── MR
├── QC
└── specs
└── parameters_example.txt
By the way, all subjects were showed the same error with JSON files. Is this because I changed the file name, causing it to be inconsistent with the parameter names of the JSON file?
Best,
Can you run import on one subject only, show the BIDS structure only for that one, along with the exact command, the logs and the session file if it gets created.
The problem seems to be in the contents of the .json files. In the log the exact location is pinpointed (line 17 column 32 (char 610)). This seems like an issue with input data and not a QuNex issue, so you will probably need to fix whatever is in there.
BIDS is a precisely defined structure, where things need to be properly defined, this also holds for the contents of JSON files. If things are not like they should be, then onboarding BIDS will not work…
Best, Jure
yzhong
July 7, 2025, 2:10am
12
Hi Jure,
Thanks for your explaination. I have fixed this error in my .json files, but there have another error in
mapBIDS2behavior step:
.......................... Running QuNex v1.1.1 [QIO] ..........................
--- Full QuNex call for command: import_bids
qunex import_bids --sessionsfolder="/hdd1/qunex/cimt/validation2/sessions" --inbox="/hdd1/qunex/cimt/validation2/rawdata/For_ProfHui/MRI_data" --archive="leave" --overwrite="yes" --sessions="HOH002_pre"
---------------------------------------------------------
started running import_bids at 2025-07-07 09:56:53, track progress in /hdd1/qunex/cimt/validation2/processing/logs/comlogs/tmp_import_bids_2025-07-07_09.56.53.134953.log
call: gmri import_bids sessionsfolder="/hdd1/qunex/cimt/validation2/sessions" inbox="/hdd1/qunex/cimt/validation2/rawdata/For_ProfHui/MRI_data" archive="leave" overwrite="yes" sessions="HOH002_pre"
-----------------------------------------
Running import_bids
==================
---> identifying files in /hdd1/qunex/cimt/validation2/rawdata/For_ProfHui/MRI_data
---> Inbox type: inbox
---> Paths:
bidsinfo -> /hdd1/qunex/cimt/validation2/info/bids
bidsinbox -> /hdd1/qunex/cimt/validation2/sessions/inbox/BIDS
bidsarchive -> /hdd1/qunex/cimt/validation2/sessions/archive/BIDS
---> mapping files to QuNex bids folders
---> bids for session 1 already exists: cleaning session
Running map_bids2nii for subject 1
==================================
---> cleaned nii folder, removed existing files
---> removed existing session.txt file
---> linked 1.nii.gz <-- HOH002_pre_ses-1_PA_dwi.nii.gz
---> ERROR: bval/bvec files were not found and were not mapped: 1.bval/.bvec <-- HOH002_pre_ses-1_PA_dwi.bval/.bvec
---> linked 2.nii.gz <-- HOH002_pre_ses-1_AP_dwi.nii.gz
---> WARNING:
Not all actions completed successfully!
Some files for session 1 were not mapped successfully!
Please check logs and data!
Running mapBIDS2behavior for subject 1
======================================
Final report
============
subject 1 image mapping failed, behavioral files: no files mapped
---> ERROR in completing import_bids:
Some actions failed
Please check report!
-----------------------------------------
Finished at 2025-07-07 09:59:02
And here is my data structure:
.
├── anat
│ ├── HOH002_pre_T1w.json
│ ├── HOH002_pre_T1w.nii
│ ├── HOH002_pre_T2w.json
│ └── HOH002_pre_T2w.nii
├── dwi
│ ├── HOH002_pre_ses-1_AP_dwi.bval
│ ├── HOH002_pre_ses-1_AP_dwi.bvec
│ ├── HOH002_pre_ses-1_AP_dwi.json
│ ├── HOH002_pre_ses-1_AP_dwi.nii
│ ├── HOH002_pre_ses-1_PA_dwi.json
│ └── HOH002_pre_ses-1_PA_dwi.nii
└── func
├── HOH002_pre_task-rest_dir-AP_run-01_bold.json
└── HOH002_pre_task-rest_dir-AP_run-01_bold.nii
Furthermore, I would like to know if Qunex can operate normally in the absence of the .bval and .bvec files? (As you can see, some of our data are missing both of them…)
Best,
Hi Acacius,
Neither the HCP Pipelines diffusion preprocessing nor the QuNex legacy DWI preprocessing will work without .bval and .bvec files.
I am also not aware of any other diffusion pipelines that will work with such thata for that matter. .bval and .bvec files tell how each diffusion-weighted image was acquired (strength and direction). Without that, preprocessing, modeling, and metric computations are impossible.
Your workaround for the issue is to keep only the AP image and use the QuNex’s legacy DWI preprocessing for diffusion.
Best, Jure
yzhong
July 7, 2025, 6:50am
14
Thanks. Now the DWI data has been successfully imported, but it seems that there was an error when importing the BOLD data:
started running import_bids at 2025-07-07 14:42:27, track progress in /hdd1/qunex/cimt/validation2/processing/logs/comlogs/tmp_import_bids_2025-07-07_14.42.27.700035.log
call: gmri import_bids sessionsfolder="/hdd1/qunex/cimt/validation2/sessions" inbox="/hdd1/qunex/cimt/validation2/rawdata/For_ProfHui/MRI_data" archive="leave" overwrite="yes" sessions="HOH002_pre"
-----------------------------------------
Running import_bids
==================
---> identifying files in /hdd1/qunex/cimt/validation2/rawdata/For_ProfHui/MRI_data
---> Inbox type: inbox
---> Paths:
bidsinfo -> /hdd1/qunex/cimt/validation2/info/bids
bidsinbox -> /hdd1/qunex/cimt/validation2/sessions/inbox/BIDS
bidsarchive -> /hdd1/qunex/cimt/validation2/sessions/archive/BIDS
---> mapping files to QuNex bids folders
---> bids for session 1 already exists: cleaning session
Running map_bids2nii for subject 1
==================================
---> cleaned nii folder, removed existing files
---> removed existing session.txt file
---> linked 1.nii.gz <-- HOH002_pre_ses-1_AP_dwi.nii.gz
Running mapBIDS2behavior for subject 1
======================================
Final report
============
subject 1 image mapping completed, behavioral files: no files mapped
-----------------------------------------
Finished at 2025-07-07 14:44:44
---> Successful completion of task
In addition, the data imported into the “sessions” folder seems to have been transformed into mere numbers instead of the original participant identifiers. What could be the reason for this?(linked 1.nii.gz ← HOH002_pre_ses-1_AP_dwi.nii.gz)
Best,
I do not see any errors in the snippet you pasted. Can you paste the session.txt file for this session?
In the QuNex study folder inside each session you should have a bids subfolder where the names are preserved and also a nii folder that uses QuNex naming conventions (e.g., numerical bold representations). QuNex internally uses its own logic for linking things together as BIDS can be quite verbose and clunky for derivatives and processing. That is normal. Once you prepare everything and start processing through HCP Pipelines, you will get a hcp subfolder that uses the HCP folder structure and that one should be familiar to you from previous studies you did.
Best, Jure
yzhong
July 7, 2025, 10:40am
16
I see, thanks. And here is my session file:session.txt (251 Bytes)
Best,
That is the correct result for onboarding what you showed above:
└── 1
└── bids
└── dwi
├── HOH002_pre_ses-1_AP_dwi.bval
├── HOH002_pre_ses-1_AP_dwi.bvec
├── HOH002_pre_ses-1_AP_dwi.json
└── HOH002_pre_ses-1_AP_dwi.nii.gz
DWI is the only image here…
yzhong
July 7, 2025, 11:09am
18
Thank you for your explanation. Now I completely understand!
Best, Acacius
Great, glad we resolved your issues.
Best, Jure
yzhong
July 8, 2025, 6:05am
20
Hi Jure,
I still have a question about this command – Should all the data(including T1, T2, dwi and BOLD image) be imported in this step? I found that there is no BOLD data but dwi data in my nii folder.
>/hdd1/qunex/cimt/validation2/sessions$ tree
.
├── 1
│ ├── behavior
│ ├── bids
│ │ ├── bids2nii.log
│ │ └── dwi
│ │ ├── HOH002_pre_ses-1_AP_dwi.bval
│ │ ├── HOH002_pre_ses-1_AP_dwi.bvec
│ │ ├── HOH002_pre_ses-1_AP_dwi.json
│ │ └── HOH002_pre_ses-1_AP_dwi.nii.gz
│ ├── nii
│ │ ├── 1.bval
│ │ ├── 1.bvec
│ │ ├── 1.json
│ │ └── 1.nii.gz
│ └── session.txt
├── archive
│ ├── behavior
│ ├── BIDS
│ ├── EEG
│ ├── HCPLS
│ └── MR
├── inbox
│ ├── behavior
│ ├── BIDS
│ ├── concs
│ ├── EEG
│ ├── events
│ ├── HCPLS
│ └── MR
├── QC
└── specs
└── parameters_example.txt
21 directories, 11 files
where 1.nii is also dwi data(seems like repeated import)
Best,
No, your import is correct. Things are imported once and then linked together so you also have everything browsable in the BIDS structure.
Yes, if your onboarding sesions also has structural data and BOLD data those should be onboarded on that.
This thread turned into chaos and you are jumping all over the place, so I have no idea where you are onboarding from and what the used command call is. Can you please:
Organize a single session into BIDS structure, put it into a separate folder and remove all the zip and other archives you have there.
List the structure of that session here.
Onboard that single session and list the exact used call.
Check the results.
Best, Jure
). Can you paste the example