Summary of what happened: I am running fmriprep on my data with fieldmap (2 magnitude images + 1 phase diff image). The output image looks weird, and very distorted. Any idea on possible reason? Command used (and if a helper script was used, a link to the helper script or the command generated): e…

Hi @e0046902 , I have relabeled your post as Software Support and added the corresponding post template, please fill in the other requested information by editing your so we an best help. Also, in the Screenshots section, please post the SDC images from the HTML report. Best, Steven

hi @Steven @Chris_Rorden , thank you. I have populated the related fields in the form, except the picture of the output from preprocessing. I deleted that previously but should be able to upload it later. Otherwise, I have provided all required information. Thank you very much for your help!

Maybe this thread can enlighten you? [image] Making Sure that the SDC has well-Applied @jsein Thank you so much again for your time and the detailed guidance. I have applied SDC using fMRIPrep LTS v20.2.7 as suggested, the output looks pretty reasonable. […

Hi @jsein @Steven , I tried skull-stripping only the phasediff image before feeding it into fmriprep, and the output is still very distorted: [image]

Indeed, I looked at your dataset and tried fmriprep v23 vs fmriprep v20.2.6 on your raw data and the difference is dramatic: Référence image, not corrected for SDC: [Capture d’écran 2023-04-19 à 01.02.59] Référence SDC-corrected: fmriprep v20.2.6: [Capture d’écran 2023-04-19 à 01.03.08] Référ…

@jsein Thanks. So would it be right to say fmriprep v23 is not suitable for use with magnitude+phasediff fieldmap correction?

I’m having what looks like the same issue. Used fMRIPrep v23 and got “corrected” BOLD images that look quite distorted in posterior areas around the occipital lobe: [image] sub-NTR0019_task-words_run-01_desc-sdc_bold.svg | Powered by Box Any new info on this iss…

Please try fmriprep v23.0.2 where a fix may have solved this issue: [image] Image orientation and PE direction for fMRIPrep Software Support I had assumed they were reversed because the phase encoding direction given in the json file for the fmap is opposite (…

Thanks @jsein , and apologies for not being more clear. I did use the latest version: About fMRIPrep version: 23.0.2 fMRIPrep command: /opt/conda/bin/fmriprep /home/cmccabe/data/NTR/data/NTR0019_bids /home/cmccabe/data/NTR/data/work participant --participant-label NTR0019 --fs-license-file /home/w…

Thank you @wwgraves for sharing this example of SDC going wrong with fmriprep v 23.0.2! Do you confirm that the SDC correction method used in your case by fmriprep v23.0.2 is the “phase difference” case? May you try with fmriprep v20.2.7 and confirm that the SDC correction is still much better with…

Fieldmap correction gone wrong

Software Support

jsein April 16, 2023, 9:28pm 4

Maybe this thread can enlighten you?