fMRIprep BOLD brain mask issue

Hello,

We are running into an issue where the functional brain mask looks like it is missing parts of the medial and lateral temporal lobes. There is signal dropout in these areas although there is presumably some small signal there we would like to keep included. This is an issue in all of our preprocessed subjects (n=10).

Is there anyway to modify the fMRIprep command so that the brain mask is not cut off?

Thank you,
Catherine

Files

Here is an image of the functional brain mask generated from fMRIprep overlaid on the prepreprocessed BOLD data for one subject.

Here is an image of the functional brain mask generated from fMRIprep overlaid on the MNI brain for one subject.

fMRIprep command (version 21.0.1)

SINGULARITY_CMD=“singularity run --cleanenv
–bind ${MAIN_DIR}:/home
–bind $BIDS_DIR:/data
–bind $SCRATCH_DIR:/work
$FMRIPREPIMAGE”

cmd="${SINGULARITY_CMD}
–participant-label $subject
–ignore fieldmaps slicetiming
–bids-filter-file /data/sen.json
–fs-license-file /data/derivatives/license.txt
–fs-subjects-dir /data/derivatives/T1
–fs-no-reconall
–bold2t1w-dof 6 --nthreads 8 --omp-nthreads 8
–work-dir /work
–write-graph --notrack -v
/data/nifti_test /data/derivatives/FMRI_Sentences participant"

Hi,

A few things:

  1. Do you have Freesurfer outputs you can use? I see you’ve added the –fs-no-reconall flag. With FreeSurfer outputs you can get some good boundary based registration to align BOLD and T1.
  2. Does the original or preprocessed BOLD signal look like there is signal dropout in those areas?
  3. Are you doing any susceptibility distortion correction? I see you are ignoring fieldmaps, so I would guess not. This could also help. If you do not have fieldmaps, you can try the fieldmap-less method (--use-syn).
  4. I believe version 21.0.2. improved BOLD masking workflows.

Best,
Steven

Hello Steven,

Thank you for your response.

  1. Do you have Freesurfer outputs you can use? I see you’ve added the –fs-no-reconall flag. With FreeSurfer outputs you can get some good boundary based registration to align BOLD and T1.
  • Yes we had previously run Freesurfer so I will move those data to our output folder.
  1. Does the original or preprocessed BOLD signal look like there is signal dropout in those areas?
  • Unfortunately yes, there is signal dropout in those areas in both the original and preprocessed data. We were hoping there was some way to preserve the signal there in the brain mask despite it being small.
  1. Are you doing any susceptibility distortion correction? I see you are ignoring fieldmaps, so I would guess not. This could also help. If you do not have fieldmaps, you can try the fieldmap-less method (--use-syn).
  • Yes, our data were PURE corrected on the scanner therefore those files have been passed as the “original” data to fMRIprep
    .
  1. I believe version 21.0.2. improved BOLD masking workflows.
  • I will upgrade our version

Hello Steven,

Thank you again for your guidance. I pointed fmriprep to our processed freesurfer data and did see a slight improvement in the brain mask around the MTL (red = freesurfer output included, blue = original). Unfortunately, we are still missing part of the MTL which is critical for our study. There is also some additional pia matter in the mask. I am waiting for the newest version of fmriprep to become available on the server I am working on, therefore I have not tried running fmriprep again using that.

In the meantime, is there a way to pass along a precomputed brain mask to fmriprep, similar to passing along a brain-extracted T1?

Screen Shot 2022-06-06 at 10.33.30 AM

Thank you,
Catherine