Hello everyone, I’m currently attempting to process my multi-echo data using version 23.1.3, following a previous error-free run with version 21.0.1. However, the output from version 21.0.1 presented a skull-stripping issue (not necessary for this question though, Inaccurate alignment of EPI and T1 )…

Hi @ByeolKLux , [image] ByeolKLux: However, I have come across other examples with varying settings in NeuroStarts, including: "B0FieldIdentifier": "B0map", "B0FieldSource": "B0map" "B0FieldSource": "phdiff_fmap", "B0FieldSource": "phdiff_fmap" All of these are synonymous. The B0FieldIdenti…

Hi Steven, Thanks for your clear answer! Then the name is arbitrary. Good to know. The participants have one set of AP/PA and 7 runs with 3 different echo times, resulting in 21 BOLD runs. fmap sub-07_ses-1_acq-mb3_dir-ap_run-01_epi.json sub-07_ses-1_acq-mb3_dir-ap_run-01_epi.nii.gz sub-07_ses-1…

Thanks for explaining! May you also share the contents of the two fmap JSON files?

Sure, here you go. { "AcquisitionMatrixPE": 82, "AcquisitionNumber": 1, "AcquisitionTime": "08:37:57.722500", "BandwidthPerPixelPhaseEncode": 24.888, "BaseResolution": 82, "BodyPartExamined": "BRAIN", "CoilCombinationMethod": "Sum of Squares", "ConsistencyInfo": "N4_VE11E_LATEST_201…

I think the problem is that you have two files with the same FieldIdentifier.

Shouldn’t the AP/PA have the same B0FieldIdentifier?

I can confirm the AP/PA epi’s having the same B0FieldIdentifier string works with my data.

What happens when you run your data using sdcflows.utils.wrangler.find_estimators? ( docs ) (you can use the package provided in the fmriprep container. can open up a python repl using singularity exec --cleanenv --bind ${BIDS_DIR},${WORK_DIR},${FREESURFER_DIR} $FMRIPREP_IMG python) E.g. >>> fro…

[image] ajschadler: I can confirm the AP/PA epi’s having the same B0FieldIdentifier string works with my data. Thanks, good to know! (I have mainly used IntendedFor so my knowledge is limited). Are you sure that both fmap files are being used in that case, and not just the reverse-phase encod…

Yep, they both are used. Both epi maps are used as topup input. No bold images need to be used (unless you only have one epi img).

How to set B0FieldIdentifier and B0FieldSource?

Software Support

jsein October 18, 2023, 8:33pm 13

Hi,

According to this thread (and linked threads), it seems that you just need to link the first echo to the fieldmap files, with either IntendedFor or B0FieldSource/B0FieldIdentifier :

I hope you will quickly find what went wrong for your dataset!

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