Error occurs when using two phase images and two magnitude images as fieldmap inputs

[wangboc]

Hi, according to BIDS naming convention, I use two magnitude and phase images as the fieldmap inputs. While, fmriprep failed to run at the beginning. The error infos :

And my inputs structure is:

[effigies]

Hi, what version of fMRIPrep are you running?

[wangboc]

should be the newest version: 1.1.1

[chrisgorgo]

@oesteban does FMRIPREP support phase1/phase2 type of SDC input data? I could not find traces of it in the codebase.

[wangboc]

How can I calculate the phase difference image by using the two phase image? I find the fslcomplex is so complex to run... :) @chrisfilo

[mattcieslak]

So does this mean that BIDS section 8.9.2 isn't currently supported?

[effigies]

@mattcieslak I believe that's correct. We would be happy to review a patch, however.

[mattcieslak]

Happy to write a workflow for this. Would it make sense to calculate a phasediff image from the two phases and send that as input to the workflow for 8.9.3-style fieldmaps? Or is there something fundamentally different between derived phasediffs and those that come from scanners?

[effigies]

I'm not really sure, myself. I have dug into the fieldmap math much less than @oesteban, who might have thoughts here.

[mattcieslak]

It looks like there is support for phase1/phase2 in the dipy workflow (https://github.com/nipy/nipype/blob/master/nipype/workflows/dmri/fsl/utils.py#L645). Would it make sense to check if the type is "phase" and if so send the two phase images to pha2rads?

Maybe it would be good to change the type from "phase" to "phases" or something more descriptive?

[oesteban]

It's been a long way @wangboc, but this has been finally addressed and released with version 1.5.1 (although you should go with the newest 1.5.2).

Could you check whether this is working out for you now? Please reopen if you find any issues.