Summary of what happened: Hello everyone! Could you help me solve my problem? I have one fMRI (json: “PhaseEncodingDirection”: “i”, “ImageOrientationText”: “Tra>Cor(-21.6)>Sag(1.6)”) and three fmap - magnitude1 (json: “PhaseEncodingDirection”: “j-”), magnitude2 (json: “PhaseEncodingDirection”: “j-…

Hi, it looks like you are in the case of phase difference map , which is not a case where FSL topup is used but rather FSL PRELUDE as it can been seen here (look for function: init_phdiff_wf). I don’t think that it is a problem to have your phase difference image with different phase encoding direct…

How are your native functional images? Are the distorsions really along the L-R direction (meaning that the phase encoding direction is really “i” or “-i” )? Which version of fmriprep are you using?

My understanding is that one set of images was acquired with AP axis and the other LR. The assumption of TOPUP and similar tools is that the truth lies precisely in the middle of the two phase reversed images (e.g. A>P and P>A or alternatively L>R and R>L). This axiom does not work if the image pair…

Thanks for this detailed report. Is there any chance you’d be willing to share the data? I’ve opened Potential issue when (phase difference) fieldmap PE orientation does not match EPI · Issue #325 · nipreps/sdcflows · GitHub where this issue can be tracked. One diagnostic for whether this is potent…

Hi @Chris_Rorden , indeed, according the the initial post, the GRE-EPI sequence used for functional images seems to have been acquired in LR whereas the set of images acquired with the GRE recalled sequence seems to have been acquired with the phase direction along the AP direction. I use intensively…

I’m very confident this doesn’t have anything to do with the phase encode direction, and is just a manifestation of the SDC regression that has been noted elsewhere. I am using the same technique: phase difference field map GRE acquisition with phase encoding i, and my bold acquisition has phase enc…

All 60 datasets have been completed with 20.2.7 with very good results. Again I can send example data of cases where the SDC regressed if that is helpful.

Yes, example data will be very useful. However is best for you to share it, you can send a link to this username @ gmail.

Hello, dear colleagues. I apologize for the long answer - I had to set up a virtual machine for data processing this files. I am new to working with the fmriprep, so I will write a sequence of actions. I use fMRIPrep 22.1.1. Before running the script, I add the following lines to the json-files: 1…

Hi, For this kind of fieldmaps, users seem to have better luck with fmriprep LTS v20.2.7: Here is an example of such report: [image] SDC using phasediff stretches signals to nonbrain areas Hi @themeo , I had figured what was most likely causing this issue w…

PhaseEncodingDirection "i" and "j-" in .json file

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jsein February 20, 2023, 8:10am 14

Hi,

For this kind of fieldmaps, users seem to have better luck with fmriprep LTS v20.2.7:

Here is an example of such report: