Hey everyone!
I am using HeuDiConv to convert my raw data to BIDS-valid format. While most things work fine, I have some warnings, one of which is about INCONSISTENT_PARAMETERS between files.
Here’s a sample of my BIDS data structure for one of my subjects:
...
├── sub-07
│ ├── ses-001
│ │ ├── anat
│ │ │ ├── sub-07_ses-001_T1w.json
│ │ │ └── sub-07_ses-001_T1w.nii.gz
│ │ ├── fmap
│ │ │ ├── sub-07_ses-001_acq-func_dir-PA_run-001_epi.json
│ │ │ ├── sub-07_ses-001_acq-func_dir-PA_run-001_epi.nii.gz
│ │ │ ├── sub-07_ses-001_acq-func_dir-PA_run-002_epi.json
│ │ │ ├── sub-07_ses-001_acq-func_dir-PA_run-002_epi.nii.gz
│ │ │ ├── sub-07_ses-001_acq-func_dir-PA_run-003_epi.json
│ │ │ └── sub-07_ses-001_acq-func_dir-PA_run-003_epi.nii.gz
│ │ ├── func
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-001_bold.json
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-001_bold.nii.gz
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-001_events.tsv
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-001_sbref.json
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-001_sbref.nii.gz
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-002_bold.json
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-002_bold.nii.gz
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-002_events.tsv
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-002_sbref.json
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-002_sbref.nii.gz
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-003_bold.json
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-003_bold.nii.gz
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-003_events.tsv
│ │ │ ├── sub-07_ses-001_task-backtothefuture_run-003_sbref.json
│ │ │ └── sub-07_ses-001_task-backtothefuture_run-003_sbref.nii.gz
│ │ └── sub-07_ses-001_scans.tsv
│ └── ses-002
│ ├── anat
│ │ ├── sub-07_ses-002_T1w.json
│ │ └── sub-07_ses-002_T1w.nii.gz
│ ├── fmap
│ │ ├── sub-07_ses-002_acq-motor_dir-PA_epi.json
│ │ ├── sub-07_ses-002_acq-motor_dir-PA_epi.nii.gz
│ │ ├── sub-07_ses-002_acq-pRF_dir-PA_epi.json
│ │ ├── sub-07_ses-002_acq-pRF_dir-PA_epi.nii.gz
│ │ ├── sub-07_ses-002_acq-tonotopy_dir-PA_epi.json
│ │ └── sub-07_ses-002_acq-tonotopy_dir-PA_epi.nii.gz
│ ├── func
│ │ ├── sub-07_ses-002_task-motor_run-001_bold.json
│ │ ├── sub-07_ses-002_task-motor_run-001_bold.nii.gz
│ │ ├── sub-07_ses-002_task-motor_run-001_events.tsv
│ │ ├── sub-07_ses-002_task-motor_run-001_sbref.json
│ │ ├── sub-07_ses-002_task-motor_run-001_sbref.nii.gz
│ │ ├── sub-07_ses-002_task-motor_run-002_bold.json
│ │ ├── sub-07_ses-002_task-motor_run-002_bold.nii.gz
│ │ ├── sub-07_ses-002_task-motor_run-002_events.tsv
│ │ ├── sub-07_ses-002_task-motor_run-002_sbref.json
│ │ ├── sub-07_ses-002_task-motor_run-002_sbref.nii.gz
│ │ ├── sub-07_ses-002_task-pRF_run-001_bold.json
│ │ ├── sub-07_ses-002_task-pRF_run-001_bold.nii.gz
│ │ ├── sub-07_ses-002_task-pRF_run-001_events.tsv
│ │ ├── sub-07_ses-002_task-pRF_run-001_sbref.json
│ │ ├── sub-07_ses-002_task-pRF_run-001_sbref.nii.gz
│ │ ├── sub-07_ses-002_task-pRF_run-002_bold.json
│ │ ├── sub-07_ses-002_task-pRF_run-002_bold.nii.gz
│ │ ├── sub-07_ses-002_task-pRF_run-002_events.tsv
│ │ ├── sub-07_ses-002_task-pRF_run-002_sbref.json
│ │ ├── sub-07_ses-002_task-pRF_run-002_sbref.nii.gz
│ │ ├── sub-07_ses-002_task-pRF_run-003_bold.json
│ │ ├── sub-07_ses-002_task-pRF_run-003_bold.nii.gz
│ │ ├── sub-07_ses-002_task-pRF_run-003_events.tsv
│ │ ├── sub-07_ses-002_task-pRF_run-003_sbref.json
│ │ ├── sub-07_ses-002_task-pRF_run-003_sbref.nii.gz
│ │ ├── sub-07_ses-002_task-tonotopy_run-001_bold.json
│ │ ├── sub-07_ses-002_task-tonotopy_run-001_bold.nii.gz
│ │ ├── sub-07_ses-002_task-tonotopy_run-001_events.tsv
│ │ ├── sub-07_ses-002_task-tonotopy_run-001_sbref.json
│ │ ├── sub-07_ses-002_task-tonotopy_run-001_sbref.nii.gz
│ │ ├── sub-07_ses-002_task-tonotopy_run-002_bold.json
│ │ ├── sub-07_ses-002_task-tonotopy_run-002_bold.nii.gz
│ │ └── sub-07_ses-002_task-tonotopy_run-002_events.tsv
│ └── sub-07_ses-002_scans.tsv
...
When I run the BIDS validator:
sudo docker run --rm -v path/to/bids:/data:ro bids/validator /data --verbose
I get a warning (along with others that I understand):
...
2: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
./sub-01/ses-001/func/sub-01_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-01/ses-002/func/sub-01_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-02/ses-001/func/sub-02_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-02/ses-002/func/sub-02_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-03/ses-001/func/sub-03_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-03/ses-001/func/sub-03_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-03/ses-002/func/sub-03_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-04/ses-001/func/sub-04_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-04/ses-001/func/sub-04_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-05/ses-001/func/sub-05_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-05/ses-001/func/sub-05_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-05/ses-002/func/sub-05_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-06/ses-001/func/sub-06_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-06/ses-001/func/sub-06_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-06/ses-002/func/sub-06_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-07/ses-001/func/sub-07_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-07/ses-001/func/sub-07_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-07/ses-002/func/sub-07_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-08/ses-001/func/sub-08_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-08/ses-001/func/sub-08_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-09/ses-001/func/sub-09_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-09/ses-001/func/sub-09_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-09/ses-002/func/sub-09_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-10/ses-001/func/sub-10_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-10/ses-002/func/sub-10_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-11/ses-001/func/sub-11_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-11/ses-001/func/sub-11_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-11/ses-002/func/sub-11_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-12/ses-001/func/sub-12_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-12/ses-001/func/sub-12_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-12/ses-002/func/sub-12_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-13/ses-001/func/sub-13_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-13/ses-001/func/sub-13_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-13/ses-002/func/sub-13_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-14/ses-001/func/sub-14_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-14/ses-001/func/sub-14_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-14/ses-002/func/sub-14_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-16/ses-001/func/sub-16_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-16/ses-001/func/sub-16_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-16/ses-002/func/sub-16_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
./sub-17/ses-001/func/sub-17_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-17/ses-001/func/sub-17_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-19/ses-001/func/sub-19_ses-001_task-backtothefuture_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1522 (voxels).
./sub-19/ses-001/func/sub-19_ses-001_task-backtothefuture_run-003_bold.nii.gz
The most common set of dimensions is: 106,106,72,1360 (voxels), This file has the dimensions: 106,106,72,1608 (voxels).
./sub-19/ses-002/func/sub-19_ses-002_task-motor_run-002_bold.nii.gz
The most common set of dimensions is: 106,106,44,467 (voxels), This file has the dimensions: 106,106,44,469 (voxels).
...
Here are the versions of my packages:
Docker version 24.0.5, build ced0996
bids-validator 1.14.6
heudiconv 1.1.0
I double-checked the actual size of the files with AFNI 3dinfo command and they seem correct to me: 1360, 1522, and 1608 for runs 1, 2, and 3, respectively.
I’m unsure why it says, “The most common set of dimensions is: 106,106,72,1360” when I have three different runs for the task ‘backtothefuture,’ and each run has its own number of TRs. The dimensions (106,106,72,1360) are correct for run-001, but for run-002 and run-003, they are 1522 and 1608, respectively. Why does the BIDS validator consider the dimensions from the first run as the most common ones?
Should I be concerned about this? Any advice or recommendations would be helpful 
Best,
Egor