I used dicm2nii to convert my files, and I have manually changed the -y direction from Phase Encoding to -j. However, when I try to run fmriprep - I am receiving the error that the field map information is incorrect (see error below). I collected the data on a GE scanner. The radiographer labelled the files blip-up and blip-down, however the .json file always reported PhaseEncoding to be -y in all files.
Can you tell me if I have to enter this data manually, or whether I should have used a different software to convert my files? How can I fix this PhaseEncoding error?
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 258, in _bootstrap
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 93, in run
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 510, in build_workflow
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 202, in init_fmriprep_wf
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 458, in init_single_subject_wf
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py”, line 401, in init_func_preproc_wf
debug=debug, fmap_demean=fmap_demean, fmap_bspline=fmap_bspline)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/base.py”, line 178, in init_sdc_wf
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/pepolar.py”, line 97, in init_pepolar_unwarp_wf
raise Exception("None of the discovered fieldmaps has the right "
Exception: None of the discovered fieldmaps has the right phase encoding direction. Possibly a problem with metadata. If not, rerun with ‘–ignore fieldmaps’ to skip distortion correction step.