fMRIPrep for 7T data

Software Support
1

Summary of what happened:

Hi all,

I am preprocessing 7T task-fMRI data with fMRIPrep, and I am trying to understand whether the output I am seeing is expected for 7T EPI or whether it suggests a problem in acquisition / preprocessing. I am new to both fmriprep and 7T data, I used to work with 3T data.

My main concern is that in the preprocessed BOLD images, the inferior part of the volume looks very abnormal, with strong signal loss / smearing / deformation below the brain (image attached). This appears both when I run fmriprep with fieldmap-based distortion correction and when I rerun it ignoring the fieldmap. I wonder if this is due to the loss of signal in the original bold (image attached)?

fmriprep_preprocessed_bold
fmriprep_preprocessed_bold1483×369 36 KB

original_bold
original_bold721×873 32 KB

Any advice would be very appreciated.

Thanks!

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

command = [
    "python", "-m", "fmriprep_docker",
    bids_root,                           
    derivatives_root,                    
    "participant",
    "--participant-label", subject_label,
    "--fs-license-file", fs_license_file,
    "--output-spaces", "T1w", "MNI152NLin2009cAsym",
    "--skip-bids-validation",         
    #"--work-dir", os.path.join(bids_root, "derivatives", "work"),
    #"--use-syn-sdc",
    "--ignore", "fieldmaps",
    "--nprocs", "1",                     
    "--omp-nthreads", "2",               
    "--low-mem"         
]

Version:

version 25.1.3

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

Docker-Desktop

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

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

fmriprep_brain mask
fmriprep_brain mask1831×813 353 KB

2

Hi @MCS and welcome to neurostars!

In the future please use the Software Support post category and template to structure your software-related posts. You can see I edited in for you this time, and there is some relevant information for these type of issues that were not provided in your initial post.

Are you using the most up-to-date version, and is the brain mask accurate? If so, then I think this is okay.

Best,
Steven

3

Hi Steven!

Thank you for your reply and your edits to my post!

I have updated it with the command I used, the fmriprep version (25.1.3 - I just realized it’s not the most up to date but it is the same I used for my previous subjects) and with a screenshot of the brain mask (the inferior part is cut off but for the rest I’d say it looks ok).

Thanks again!

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