Creating FMRIPREP-ready Pepolar Scans for Distortion Correction (GE)

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I was having some issues with alignment and you guys recommended getting phase encoding scans for distortion correction. Well I ended up adding that to my protocol except we use the worst scanner make (GE) and I’ve never used phase encoding scans before so I’d just like to make sure I’m creating the right files for use in the pipeline. My scans are 2 pepolar scans per run (so 3 total as I have 3 runs). I have read every thread with the word “pepolar” in it and here’s what I have come up with in terms of questions and conclusions.

  1. I’ll start with the world’s stupidest question: Can you make the field maps by simply running dcm2niix? Running this on my pepolar scans gives the same output including the same “PhaseEncodingAxis”: “I” and “InPlanePhaseEncodingDirectionDICOM”: “ROW” so I’m not sure if this is the correct first step.

  2. Given the above info it seems easiest to create the .json files as Chris made them here with just these 3 parameters and running dcm2niix does give “TotalReadoutTime”: 0.025956. Would it be ok to run dcm2niix on the .dcm files, scrap the .json files it makes, make one from scratch with the parameters in Chris’ files? Or is there a better way? If this is in fact the easiest way, how does one go about figuring out which scan direction is ‘I’ and which is ‘I-’ given this minimal GE information. I should note that when I download my scans I get this screen (below) which tells me the pepolar=1 scan is probably the reverse polarity scan. Should I just eat it and hard-code all of these scans as “I-” or is there an easier way?

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  3. Once you’ve made your initial field maps with dcm2niix or whatever, do you need to edit them in any way? I saw in this thread something about ‘cutting’ longer scans but I think this is for EPIs (not distortion correction?) but just wanted to make sure.

  4. Finally, once the maps are made and “processed” you use BOTH of them for each scan, correct?I’m looking at Chris’ example dataset from the first link and, for example, he has a file named “sub-100307_acq-EMOTIONLR_dir-1_epi.json” which is encoded in the “I-” direction and sub-100307_acq-EMOTIONLR_dir-2_epi.json which is encoded in the “I” direction that are “IntendedFor” the same .nii file so I would basically do the same thing, I imagine, with my files. So I guess my question is I use both and not just one, correct?

I’m so sorry for this really basic post - the BIDS specification tells me what the .json file should look like but not how to get there (and GE does not help).

Thank you guys for everything.
Lauren

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Hi @lhopkins

Thank you for raising this question! To answer your questions:

  1. dcm2niix should be able to handle converting your phase encoding scans to nifti format. This would be having dcm2niix convert your dicom images.

  2. I think following Chris’s directions is a good approach. The output from dcm2niix will hopefully provide the necessary fields for software like fMRIPrep to read and utilize. The scan direction I believe will be the PhaseEncodingAxis you mentioned in your first point.

  3. It appears it is for EPI as you mentioned

  4. If you have two directions (I and I-) then yes you can use both and use the IntendedFor field to indicate this (as you said).