Posterior - anterior streaks in in EPI images after fmriprep

Software Support
,
1

Summary of what happened:

Hi all,

I am a first-time user of fmriprep, and have observed an issue with several of my participants. An example co-registration image is attached — you can see a number of dark streaks, running in the posterior-anterior direction. I’ve observed this in about 20 of the 70 participants I’ve run fmriprep on, but haven’t been able to find anything else in the QA report that corresponds with this (these participants don’t have excess motion, for example). Do any of you have insight into what might be going wrong here?

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

fmriprep-docker --fs-license-file ../Software/license.txt  stagingareas/${user}  /home/${user}

Version:

23.2.1

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

Singularity

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

Sidecars were written using dcm2niix -- errors did not prevent fmriprep from running

error: SIDECAR_KEY_REQUIRED (TaskName)
warning: README_FILE_MISSING
warning: TOO_FEW_AUTHORS
warning: JSON_KEY_RECOMMENDED (DatasetType)
warning: JSON_KEY_RECOMMENDED (License)
warning: JSON_KEY_RECOMMENDED (GeneratedBy)
warning: JSON_KEY_RECOMMENDED (SourceDatasets)
warning: NO_AUTHORS (Authors)
warning: SIDECAR_KEY_RECOMMENDED (ReceiveCoilName)
warning: SIDECAR_KEY_RECOMMENDED (ReceiveCoilActiveElements)
warning: SIDECAR_KEY_RECOMMENDED (GradientSetType)
warning: SIDECAR_KEY_RECOMMENDED (MRTransmitCoilSequence)
warning: SIDECAR_KEY_RECOMMENDED (MatrixCoilMode)
warning: SIDECAR_KEY_RECOMMENDED (CoilCombinationMethod)
warning: SIDECAR_KEY_RECOMMENDED (PulseSequenceType)
warning: SIDECAR_KEY_RECOMMENDED (SequenceName)
warning: SIDECAR_KEY_RECOMMENDED (PulseSequenceDetails)
warning: SIDECAR_KEY_RECOMMENDED (MTState)
warning: SIDECAR_KEY_RECOMMENDED (SpoilingState)
warning: SIDECAR_KEY_RECOMMENDED (NumberShots)
warning: SIDECAR_KEY_RECOMMENDED (ParallelReductionFactorOutOfPlane)
warning: SIDECAR_KEY_RECOMMENDED (ParallelAcquisitionTechnique)
warning: SIDECAR_KEY_RECOMMENDED (PartialFourier)
warning: SIDECAR_KEY_RECOMMENDED (PartialFourierDirection)
warning: SIDECAR_KEY_RECOMMENDED (EffectiveEchoSpacing)
warning: SIDECAR_KEY_RECOMMENDED (MixingTime)
warning: SIDECAR_KEY_RECOMMENDED (PhaseEncodingDirection)
warning: SIDECAR_KEY_RECOMMENDED (TotalReadoutTime)
warning: SIDECAR_KEY_RECOMMENDED (DwellTime)
warning: SIDECAR_KEY_RECOMMENDED (MultibandAccelerationFactor)
warning: SIDECAR_KEY_RECOMMENDED (InstitutionAddress)
warning: SIDECAR_KEY_RECOMMENDED (InstitutionalDepartmentName)
warning: SIDECAR_KEY_RECOMMENDED (TaskName)
warning: SIDECAR_KEY_RECOMMENDED (NumberOfVolumesDiscardedByScanner)
warning: SIDECAR_KEY_RECOMMENDED (NumberOfVolumesDiscardedByUser)
warning: SIDECAR_KEY_RECOMMENDED (DelayTime)
warning: SIDECAR_KEY_RECOMMENDED (AcquisitionDuration)
warning: SIDECAR_KEY_RECOMMENDED (DelayAfterTrigger)
warning: SIDECAR_KEY_RECOMMENDED (Instructions)
warning: SIDECAR_KEY_RECOMMENDED (TaskDescription)
warning: SIDECAR_KEY_RECOMMENDED (CogAtlasID)
warning: SIDECAR_KEY_RECOMMENDED (CogPOID)
warning: SIDECAR_KEY_RECOMMENDED (ParallelReductionFactorInPlane)
warning: SIDECAR_KEY_RECOMMENDED (InversionTime)
warning: SIDECAR_KEY_RECOMMENDED (SliceEncodingDirection)
warning: EVENTS_TSV_MISSING

Relevant log outputs (up to 20 lines):

anat_only = false
aroma_err_on_warn = false
aroma_melodic_dim = 0
bold2t1w_dof = 6
bold2t1w_init = "register"
cifti_output = false
fmap_bspline = false
force_syn = false
hires = true
ignore = []
level = "full"
longitudinal = false
run_msmsulc = true
medial_surface_nan = false
project_goodvoxels = false
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "MNI152NLin2009cAsym:res-native"
use_aroma = false
use_syn_sdc = false
me_t2s_fit_method = "curvefit"

Screenshots / relevant information:

aftifact
aftifact1784×909 189 KB

2

Hi @neuro_n00b, and welcome to neurostars!

In the future please use the Software Support category which prompts you to organize your post in a way that makes it easier for us to help. I have added the template in for you this time. You can edit your post to add in the necessary information.

Best,
Steven

3

Thank you! Tried to provide the information I have… will this work?

4

Thanks, does the error persist in the most recent version? Is susceptability distortion correction being applied at all? Do the raw images (T1w and BOLD) look okay?

5

I’m not sure, but could this be a related issue to the one that I posted about here? Field map error in fmriprep v24.0.0
(I posted here and on Github but still haven’t gotten a definitive reply about it.)

6

Hi Steven,

I haven’t yet tried applying the newest version of fmriprep—have been avoiding an upgrade so that all of our data goes through the same pipeline. Notably, most participant data that’s gone through this pipeline doesn’t have this issue.

No SDC — T1w looks great, but all raw BOLD images for this participant have the same issue (across 7 runs and 4 tasks).

Screenshot (14)
Screenshot (14)929×480 15.5 KB

7

Are you saying that all images in the bad subjects look like this? Or all images across all subjects like this (and therefore improve after fmriprep)?

8

Thanks for clarifying! All images for bad participants look like this. Other participants’ BOLD files do not have this issue.

9

Thanks for clarifying - I would say that this isn’t an error in fmriprep then. This is probably something about the acquisition, but I cannot say what it might be without knowing more about how the images were collected (scanner vendor, observed motion, sequence details, etc).

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