Hi, I’m a clinical neuroscientist and I’m working with MRTrix docker. When running the project I received the following error:
dwifslpreproc: [ERROR] No phase-encoding contrast present in SE-EPI images; cannot perform inhomogeneity field estimation
mrtrix3_connectome.py:
mrtrix3_connectome.py: [ERROR] For debugging, inspect contents of scratch directory: /mrtrix3_connectome.py-tmp-VKW6EH/
mrtrix3_connectome.py: Scratch directory retained; location: /mrtrix3_connectome.py-tmp-VKW6EH/
To confirm, was the data acquired with opposing phase encoding directions? For example, one set of DWI with AP phase encoding direction, and a second with PA phase encoding direction? That’
If so, can you use mrinfo on the input files to check whether phase encoding info is embedded in the files (assuming it’s a *.mif)? If you’re using *.nii.gz as input, then make sure there’s a paired *.json file with the exact same name that has the phase encoding information too. You would then need to include the -json_import flag to include it so it can read the PE info.
