BIDS validator not finding dwi modality

Software Support
,
1

Hello,

I used dcm2bids to convert my functional, structural, and diffusion data into bids format. However, I noticed that the bids validator did not seem to find the dwi modality. It also did not throw out any errors.

Summary of what happened: web-based bids validator not finding the dwi modality. Later I also run bids validation within qsiprep, which also did not detect the dwi.

My file structure looks like this:

├── CHANGES
├── code
│   └── dcm2bids_config.json
├── dataset_description.json
├── derivatives
├── participants.json
├── participants.tsv
├── README
└── sub-220801
    ├── anat
    │   ├── sub-220801_FLAIR.json
    │   ├── sub-220801_FLAIR.nii.gz
    │   ├── sub-220801_T1w.json
    │   └── sub-220801_T1w.nii.gz
    ├── dwi
    │   ├── sub-220801_run-01_dwi.bval
    │   ├── sub-220801_run-01_dwi.bvec
    │   ├── sub-220801_run-01_dwi.json
    │   ├── sub-220801_run-01_dwi.nii.gz
    │   ├── sub-220801_run-02_dwi.bval
    │   ├── sub-220801_run-02_dwi.bvec
    │   ├── sub-220801_run-02_dwi.json
    │   └── sub-220801_run-02_dwi.nii.gz
    ├── fmap
    │   ├── sub-220801_acq-func_dir-AP_epi.json
    │   ├── sub-220801_acq-func_dir-AP_epi.nii.gz
    │   ├── sub-220801_acq-func_dir-PA_epi.json
    │   ├── sub-220801_acq-func_dir-PA_epi.nii.gz
    │   ├── sub-220801_acq-single_dir-AP_epi.bval
    │   ├── sub-220801_acq-single_dir-AP_epi.bvec
    │   ├── sub-220801_acq-single_dir-AP_epi.json
    │   ├── sub-220801_acq-single_dir-AP_epi.nii.gz
    │   ├── sub-220801_acq-single_dir-PA_epi.bval
    │   ├── sub-220801_acq-single_dir-PA_epi.bvec
    │   ├── sub-220801_acq-single_dir-PA_epi.json
    │   └── sub-220801_acq-single_dir-PA_epi.nii.gz
    └── func
        ├── sub-220801_task-rest_bold.json
        └── sub-220801_task-rest_bold.nii.gz

The bids-validator output look like this:

1730422499294
17304224992941141×900 67.2 KB

2

Hi @Catherine_Tang,

What makes it think it did not find your DWI? The file count seems accurate for reflecting DWI. DWI is under the modality of “MRI” so you wouldn’t see an additional modality, and there is no DWI task, so you wouldn’t see any additional tasks.

Best,
Steven

3

Ok that’s good to know. The reason I think it didn’t recognize was because when I run qsiprep, it did not run dwi preprocessing and it only ran T1 processing. In the summary.html:

  • Subject ID: sub-220801
  • Structural images: 1 T1-weighted
  • Diffusion-weighted series: inputs 0, outputs 0
  • Resampling targets: T1wACPC
  • FreeSurfer reconstruction: Not run

This made me wonder if it wasn’t recognizing the dwi.

4

You should make a software support post for this because there is not enough information here about your qsiprep run to diagnose an issue.

Best,
Steven