I changed the file structure to this:
Updated folder for sub_1 here:
https://drive.google.com/drive/folders/1K_hbxhR_KqQChk5E9Cy3isut87jttX1R?usp=drive_link
And still got the following error:
1: [ERR] The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files. (code: 29 - VOLUME_COUNT_MISMATCH)
./sub-1/dwi/sub-1_rec-ADC_dwi.nii.gz
./sub-1/dwi/sub-1_rec-TRACE_dwi.nii.gz
./sub-10/dwi/sub-10_rec-ADC_dwi.nii.gz
./sub-10/dwi/sub-10_rec-TRACE_dwi.nii.gz
./sub-100/dwi/sub-100_rec-ADC_dwi.nii.gz
./sub-100/dwi/sub-100_rec-TRACE_dwi.nii.gz
./sub-1000/dwi/sub-1000_rec-ADC_dwi.nii.gz
./sub-1000/dwi/sub-1000_rec-TRACE_dwi.nii.gz
./sub-1001/dwi/sub-1001_rec-ADC_dwi.nii.gz
./sub-1001/dwi/sub-1001_rec-TRACE_dwi.nii.gz
... and 3420 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=VOLUME_COUNT_MISMATCH for existing conversations about this issue.
See also : Multiple Lesion Masks for BIDS - #5 by neurolabusc
Thanks for helping me with this!
Roger