Phase encoding error for field maps

1

Hello,

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?

Many thanks,
Kaylena

Process Process-2:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 258, in _bootstrap
self.run()
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 510, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 202, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 458, in init_single_subject_wf
ignore_aroma_err=ignore_aroma_err)
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
name=‘pepolar_unwarp_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.

2

Did you run the BIDS validator on your dataset? If you’re using -j as the PhaseEncodingDirection, then the problem is just that it needs to be j-. If the validator isn’t catching that, we should open an issue. And fMRIPrep could stand to have a more explicit error indicating what it’s looking for.

If you did have j-, then does your BOLD file have PhaseEncodingDirection of j?

3

Hi Chis,

Thank you for your reply - I can confirm I have used j-. I did run the BIDS validator, and it did not produce an error, only a few warnings related to tsv files.

In regards to my BOLD files, I am not entirely sure what you are asking. When I used the dicm2nii it outputted PhaseEncodingDirection of y-, which I then manually changed to j- since this corresponds to BIDS specs. Should I have done something different?

Many thanks,

4

If I’m reading you correctly, both your fieldmaps and your BOLD series are j-? If so, that’s the problem. For blip-up/blip-down, you need your fieldmaps to be use the opposite phase-encoding direction from your BOLD series. i.e. If you BOLD series is j, then your EPI fieldmap should be j-, and vice versa.

5

Ok thanks, I will try changing my BOLD .json files to j and then the EPI.json files to j-, and see if this solves the issue.

Many thanks!