FSL epi_reg and BIDS

[Dianne Patterson]

Dear FSL and BIDS experts,

epi_reg currently expects phase encoding direction to be specified as follows:

--pedir=<dir>          : phase encoding direction, dir = x/y/z/-x/-y/-z

The BIDS standard, however, implements "PhaseEncodingDirection": "j-", like this 

(j- = -y).  

It is very useful to pull echo spacing and echo timing values directly from the json, but, unless I'm missing something, we cannot do this with phase encoding direction. 

Are there plans to address this issue either on the BIDS side or the FSL side? Or, am I missing something?

Thanks very much,

Dianne

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[Chris Gorgolewski]

To give some context: there was a lot of discussion about this pre BIDS 1.0 release and i,j,k nomenclature was chosen explicitly over x,y,z to emphasize that the direction referred to was in voxel space not real world mm space.

Changing it is possible if desired (although personally I'm not convinced it's necessary), but would have to wait for backward compatibility breaking 2.0 release.

Best,

Chris

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[Harms, Michael]

 

I would not change this in BIDS.  The i,j,k nomenclature is much more clear that the direction is specified in voxel space (i.e., is relative to the stored orientation of the NIFTI). 

 

Cheers,

-MH

 

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Michael Harms, Ph.D.

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Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

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Chris

 

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