questions > dcm2niix = how to determine blip direction from .json file
Jun 28, 2020  10:06 AM | Kathleen Hupfeld - University of Florida
dcm2niix = how to determine blip direction from .json file

I collected field map / resting state MRI data and converted from DICOM -> NII using dcm2niix. I am having difficulty interpreting the "blip direction" for my rs-MRI data based on the .json file produced by dcm2niix. 

The rs-MRI images have "PhaseEncodingDirection": "j" in the json file. This matches my P>>A field maps (j direction), and not my A>>P field maps (j- direction). 

I need the rs-MRI blip direction for use with the SPM FieldMap toolbox: 
-Toolbox manual: The VDM is multiplied by +/-1 to indicate whether the K-space traversal for the data acquisition has a +ve or -ve blip direction. This will ensure that the unwarping is performed in the correct direction. 

However, I wasn't sure how the PhaseEncodingDirection maps onto +ve vs. -ve blip direction? (i.e., does j = +ve and j- = -ve? Or is there anything more complex that I am missing?) 

There is some conflicting information online that suggests relying on visual inspection wrt blip direction
-Oregon LCNI: Polarity of the blips depends not only on your acquisition but also on how your data was converted to NIFTI, so it could be either + or - ve ( 
-Harvard: Blip direction: -1 (but really this partly depends on how you convert your dicoms, so for your first subject, you should try it both ways and see which way is better (

Any insight would be greatly appreciated. 


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dcm2niix = how to determine blip direction from .json file
Kathleen Hupfeld Jun 28, 2020
Chris Rorden Jun 28, 2020
Kathleen Hupfeld Jun 28, 2020