[RESOLVED] Import BIDS Data

Use Questions
22

Apologize for confusing the issue due to my debugging, here is my file structure and how it runs.
My complete data file structure is as follows：

├── 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
│   └── func
│       ├── HOH002_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH002_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOH003_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH003_pre_task-rest_dir-AP_run-01_bold.nii
├── HOH006_pre
│   ├── anat
│   │   ├── HOH006_pre_T1w.json
│   │   ├── HOH006_pre_T1w.nii
│   │   ├── HOH006_pre_T2w.json
│   │   └── HOH006_pre_T2w.nii
│   ├── 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
│   └── func
│       ├── HOH006_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH006_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOH011_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH011_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOH013_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH013_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOH015_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH015_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOH019_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH019_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOH020_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOH020_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOS005_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOS005_pre_task-rest_dir-AP_run-01_bold.nii
├── 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
│   └── func
│       ├── HOS006_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOS006_pre_task-rest_dir-AP_run-01_bold.nii
├── HOS007_pre
│   ├── anat
│   │   ├── HOS007_pre_T1w.json
│   │   ├── HOS007_pre_T1w.nii
│   │   ├── HOS007_pre_T2w.json
│   │   └── HOS007_pre_T2w.nii
│   ├── dwi
│   │   ├── 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
│   └── func
│       ├── HOS007_pre_task-rest_dir-AP_run-01_bold.json
│       └── HOS007_pre_task-rest_dir-AP_run-01_bold.nii
└── 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
    └── func
        ├── HOS009_pre_task-rest_dir-AP_run-01_bold.json
        └── HOS009_pre_task-rest_dir-AP_run-01_bold.nii

In order to test the complete processing procedure, I only processed the HOH002_pre participant data. My command is:

		qunex_container import_bids \
		    --sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
		    --sessions="HOH002_pre" \
		    --inbox="${RAW_DATA}" \
		    --archive="leave" \
		    --bind="/hdd1:/hdd1" \
		    --container="${QUNEX_CONTAINER}" \
		    --overwrite="yes"

And the output is:


.......................... 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" --bidsname="HOH002_pre" --overwrite="yes" --sessions="HOH002_pre"

---------------------------------------------------------


started running import_bids at 2025-07-08 15:21:20, track progress in /hdd1/qunex/cimt/validation2/processing/logs/comlogs/tmp_import_bids_2025-07-08_15.21.20.345102.log
call: gmri import_bids sessionsfolder="/hdd1/qunex/cimt/validation2/sessions" inbox="/hdd1/qunex/cimt/validation2/rawdata/For_ProfHui/MRI_data" archive="leave" bidsname="HOH002_pre" 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/MRI_data
    bidsinbox   -> /hdd1/qunex/cimt/validation2/sessions/inbox/BIDS
    bidsarchive -> /hdd1/qunex/cimt/validation2/sessions/archive/BIDS
---> mapping files to QuNex bids folders
    ---> creating bids session 1
Running map_bids2nii for subject 1
==================================
---> linked 1.nii.gz <-- HOH002_pre_ses-1_AP_dwi.nii.gz
Running mapBIDS2behavior for subject 1
======================================
---> created behavior subfolder

Final report
============
subject 1 image mapping completed, behavioral files: no files mapped

-----------------------------------------
Finished at 2025-07-08 15:23:33

---> Successful completion of task

But when I check my sessions folder, it seems only dwi data be imported:

> /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

where 1.nii is also dwi data.

Best,
Acacius

23

I think you have file naming issues as the BIDS file names are not consistent. Simplified, BIDS naming is as such: <subject>_<session>_<image>. In your case it is a bit all over the place again. For example:

  • HOH002_pre_T1w.nii.gz this seems fine, subject is HOH002, session is pre, image is T1w.
  • HOH002_pre_ses-1_AP_dwi.nii.gz you can see this is not consistent with T1w annotation, what is ses-1?
  • HOH002_pre_task-rest_dir-AP_run-01_bold.nii this is consistent with T1w, but inconsistent with DWI.

Try renaming all files as HOH002_001_<image>.nii.gz. This way it will be onboarded into QuNex as subject HOH002, session 001.

Best, Jure

24

I have renamed my data as your suggestion:

├── anat
│   ├── HOH002_001_T1w.json
│   ├── HOH002_001_T1w.nii.gz
│   ├── HOH002_001_T2w.json
│   └── HOH002_001_T2w.nii.gz
├── dwi
│   ├── HOH002_001_AP_dwi.bval
│   ├── HOH002_001_AP_dwi.bvec
│   ├── HOH002_001_AP_dwi.json
│   └── HOH002_001_AP_dwi.nii.gz
└── func
    ├── HOH002_001_task-rest_dir-AP_run-01_bold.json
    └── HOH002_001_task-rest_dir-AP_run-01_bold.nii.gz

But all of them can not be imported after unified their name:


.......................... 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" --bidsname="HOH002" --overwrite="yes" --sessions="HOH002"

---------------------------------------------------------


started running import_bids at 2025-07-08 17:50:46, track progress in /hdd1/qunex/cimt/validation2/processing/logs/comlogs/tmp_import_bids_2025-07-08_17.50.46.751713.log
call: gmri import_bids sessionsfolder="/hdd1/qunex/cimt/validation2/sessions" inbox="/hdd1/qunex/cimt/validation2/rawdata/For_ProfHui/MRI_data" archive="leave" bidsname="HOH002" overwrite="yes" sessions="HOH002"
-----------------------------------------
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/MRI_data
    bidsinbox   -> /hdd1/qunex/cimt/validation2/sessions/inbox/BIDS
    bidsarchive -> /hdd1/qunex/cimt/validation2/sessions/archive/BIDS
---> mapping files to QuNex bids folders

Final report
============

When running import_bids:
No sessions were mapped in this call. Please check report!

-----------------------------------------

Best,
Acacius

25

What is the used command call?

26

@yzhong Your filenames do not conform to the BIDS naming convention. For example, you have named one of them HOH002_001_T1w.nii.gz. It should actually be sub-HOH002_ses-001_T1w.

Please refer to the introduction to the BIDS scheme here and check the examples.

The folder should also be named sub-HOH002, and within that folder, you should have another folder named ses-001. The subject name should not contain any underscores. You can check whether your dataset is BIDS compliant using BIDS Validator.

27

Thanks Andraz! For some reason I forgot about the sub- and ses- prefixes …

28

Thank you and Andraz very much for the kindly help. Now all the problems have been solved!

Best,
Acacius