Echotime error on fmriprep

Software Support
1

Summary of what happened:

Hi everyone, I’ve read some previous posts on a similar topic, but wondering if this has been resolved at all?
I’m trying to default frmi-prep pipeline, and keep running into an issue with my fmap images - they have an EchoTime of 0.03, but fmri-prep is generating an error - posted below. Similarly, when I try BIDS validator, I’m getting this error: The value of (EchoTime2 - EchoTime1) should be within the range of 0.0001 - 0.01.
(I only have 1 Echo time, which is 0.03) - I uploaded the .json for an example image here too if it helps.

Does anyone have an easy fix for this? Hoping to run everything through one smooth pipeline.
Thank you in advance!!!

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep-docker $bids_root_dir $bids_root_dir/derivatives \
    participant \
    --participant-label $subj \
    --skip-bids-validation \
    --md-only-boilerplate \
    --fs-license-file $HOME/Desktop/FMTEST/derivatives/license.txt \
    --fs-no-reconall \
    --output-spaces MNI152NLin2009cAsym:res-2 \
    --nthreads $nthreads \
    --stop-on-first-crash \
    --mem_mb $mem_mb

Version:

22.1.0

Environment (Docker, Singularity / Apptainer, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

    /ses-preop/fmap/sub-MDD14dbs_ses-preop_task-resting_run-1_phasediff.nii.gz
    /ses-preop/fmap/sub-MDD14dbs_ses-preop_task-etoh_run-1_phasediff.nii.gz
    /ses-preop/fmap/sub-MDD14dbs_ses-preop_task-face_run-1_phasediff.nii.gz

Relevant log outputs (up to 20 lines):

240808-12:29:47,729 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['AUD1'].
           * Run identifier: 20240808-122918_c29e30cd-1c73-4236-8083-9a6011a0531d.
           * Output spaces: MNI152NLin2009cAsym:res-2.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/workflow.py", line 115, in build_workflow
    retval["workflow"] = init_fmriprep_wf()
  File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 91, in init_fmriprep_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 367, in init_single_subject_wf
    fmap_estimators = find_estimators(
  File "/opt/conda/lib/python3.9/site-packages/sdcflows/utils/wrangler.py", line 337, in find_estimators
    fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
  File "<attrs generated init sdcflows.fieldmaps.FieldmapFile>", line 12, in __init__
    self.__attrs_post_init__()
  File "/opt/conda/lib/python3.9/site-packages/sdcflows/fieldmaps.py", line 265, in __attrs_post_init__
    raise MetadataError(
sdcflows.fieldmaps.MetadataError: Missing 'EchoTime1' and/or 'EchoTime2' for </data/sub-AUD1/ses-12mos/fmap/sub-AUD1_ses-12mos_task-etoh_run-1_phasediff.nii>.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues

Screenshots / relevant information:

FMAP_Example.txt (2.7 KB)

2

Hi @Benjamin_Davidson,

In the future, please use the Software Support post category / template, which prompts you to better organize your post. You can see I edited your post to reflect that. Please edit your post to add in the missing information so we can help.

Best,
Steven

3

Hi @Benjamin_Davidson,

What you provided was not the output of the validator, but I can tell from your file structure that the data are not BIDS valid, as task-<> is not a BIDS valid label for fieldmaps.

Can you try with the most recent 24.0.1?

This flag is not recommended.

Do you have magnitude 1 and 2 images?

Best,
Steven

4

Hi Steven,
I really appreciate your replies. I believe I have figured it out. What I have is a blip-up, blip-down set of images, which I have no placed in the fmap folder, with names like: sub-1_ses-12mos_acq-face_run-1_dir-AP_epi.nii.gz, and sub-1_ses-12mos_acq-face_run-1_dir-PA_epi.nii.gz. This seems to have fixed the problem