EPI reference in fMRIPrep visual report error?

[etow6030]

Hello,

I just ran a participant through the fmirprep pipeline (fMRIPrep version: 20.2.7, latest version avail for the HPC I am working on)

< * fMRIPrep command: /usr/local/miniconda/bin/fmriprep /scratch/Predictors_MDMA_AT/MPATHY_MRI/fmriprep/bids /scratch/Predictors_MDMA_AT/MPATHY_MRI/fmriprep/prep_derivatives participant --participant_label 1115536 --fs-license-file /scratch/Predictors_MDMA_AT/MPATHY_MRI/fmriprep/Ref_Files/freesurfer.txt --bold2t1w-dof 6 --force-bbr --dummy-scans 10 --skull-strip-t1w auto --n-cpus 8 --cifti-output --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym>

The field map is a B0 acquisition map that I have spilt (using fslsplit) into the phase and magnitude. And this pipeline has worked correctly for other participants I have run through, but for some reason this participant has a weird green grid for z= 100 of the " Estimated fieldmap and alignment to the corresponding EPI reference"

Here is a screenshot of the green grid

If anyone has any idea on why this is being produced, and whether or not it means there is an error within the pipeline (or the scan itself) it would be much appreciated

Thank you!

[Steven]

Hi @etow6030,

Not a direct answer, but you should be able to install newer fmriprep containers with Singularity/Apptainer modules on your HPC, and apptainer can also be installed into a Conda/Mamba environment.

I’m not sure there’s enough info here to say whether that’s a bug with the software, raw image, or derived image. Out of the raw and derived images, which files would you see this with an image viewer?

Best,
Steven

[etow6030]

Hi Steven,

Thank you for the speedy reply

The file is sub-1115536/figures/sub-1115536_ses-01_task-restingstate_desc-fieldmap_bold.svg

I have attached an screenshot of the .svg file which might be helpful?

Thanks

[Steven]

I think as long as the final bold looks fine you have nothing to worry about. But also I recommend updating versions.