Fmriprep bold-T1w alignment in fmriprep

Software Support
,
1

Summary of what happened:

I have run fmriprep using two versions: 20.2.2 (with custom code to use align_epi_anat.py from afni to align bold to T1w) and 25.1.3. In the new version, I notice the bold anterior ventricles do not overlay completely onto the preprocessed T1w image. In the old version, the ventricle alignment looks perfect. I see this misalignment often in our nonmultiecho fmri data. Does anyone else notice a misalignment usually in the front ventricles in new fmriprep versions?

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

singularity run --cleanenv \
    -B /scratch/g/jbinder/jheffernan/experiments/tdcs/bids:/data \
    -B /scratch/g/jbinder/jheffernan/experiments/tdcs/derivatives/fmriprep-v25.1.3/fmriprep:/out \
    -B /scratch/g/jbinder/jheffernan/experiments/tdcs/derivatives/fmriprep-v25.1.3/tmp/sub-MCW052:/work \
    -B /hpc/apps/freesurfer/6.0.0/license.txt:/opt/freesurfer/license.txt \
    /scratch/g/jbinder/jheffernan/experiments/tdcs/singularity_images/fmriprep-v25.1.3.sif \
    /data /out participant \
    --participant_label MCW052 \
    --nprocs 16 \
    --omp-nthreads 4 \
    --output-spaces MNI152NLin2009cAsym:res-2 T1w \
    --no-submm-recon \
    --fs-license-file /opt/freesurfer/license.txt \
    --work-dir /work \
    --bold2anat-dof 6 \
    --fs-no-reconall \
    --ignore slicetiming

Version:

fMRIPrep 25.1.3 and fMRIPrep 20.2.2

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

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

Our dataset is in bids format and fMRIPrep successfully completes.

Screenshots / relevant information:

I’m not sure how bet to present the data, but here is the fMRIPrep 20.2.2 bold at 0.45 opacity in T1w space overlaid onto the preprocessed T1w image:

image
image1721×2322 300 KB

Here is the fMRIPrep 25.1.3 bold at 0.45 opacity in T1w space overlaid onto the same preprocessed T1w image:

image
image1721×2322 303 KB

The green crosshair is in the same location in both images. The same T1w image is used as the background in both. Notice in the second image the anterior ventricles do not complete overlap the T1w image ventricles where the crosshair is located.

Is the alignment in the second image common when preprocessing bold? I feel like there should be maximal alignment between the T1w and bold ventricles especially if we are creating a CSF regressor.

2

Hi @heffjos, was SDC correction applied in the same way between the two executions of fmriprep?It looks like the BOLD image from the 25.1.3 version is more distorded (less SDC corrected) in the frontal part of the brain.

Also the use of --fs-no-reconall is generally not recommended by the developper of fmriprep. Removing this flag allows the use of bbregister which mat improved the bold-T1w alignment, but at the expense of elongated execution time (freesurfer execution takes a while).

3

Hi @jsein

The dataset includes 2 spin echo pairs with opposing phase encoding direction for SDC. fmriprep 25.1.3 uses topup (fsl) to estimate the B0-nonuniformity map. fmriprep 20.2.2 uses 3dQwarp (afni) to estimate the B0-nonuniformity map.

I generally do use --fs-no-reconall when I can, but the dataset here is a stroke participant which may not allow freesurfer to complete and can cause a bad brainmask. Sometimes I notice similar problems when not using the --fs-no-reconall flag in some datasets. I will see if I can find a good example.

For completeness, here is an image overlaying the same preprocessed bold with fmriprep 25.1.3 but using align_epi_anat.py for registering the bold to the T1w:

image
image1721×2322 312 KB

I’d say this matches more closely to the fmriprep 25.1.3 image in my first post, so the difference could be caused the SDC methods.

4

Thank you for this detailed answer.
You may try :
--bold2anat-dof 9 or --bold2anat-dof 12 to improve the bold-to-T1w registration.