I’m trying to run dwiintensitynorm on 5 participants. I’ve created the folder structure required, and symbolically linked the denoised and preprocessed dwi data to the dwi_input folder (001_dwi_preprocessed.mif, 002_dwi_preprocessed.mif…), as well as the brain mask files to the mask_input folder (001_dwi_brain_mask.mif, 002_dwi_brain_mask.mif…). I get the following error when I run:
Perfect - this seems to solve the problem. Just FYI, there was a .DS_Store hidden file in the input_mask folder that had to be deleted as well so that the algorithm recognized an equal number of dwi and mask inputs.
EDIT: Apologies: While a fix has been implemented for MRtrix3 that instructs these scripts to ignore any hidden files in the input directories, I was mistaken in thinking that it was pushed to the master branch of MRtrix3. The fix is implemented in the development branch, and will therefore form part of the next tag release.