Dwi2mask generates full-white mask instead of brain

[Javier]

Hello,

The code below is part of my preprocessing pipeline, which I ran in Neurodesk using MRtrix3 (version 3.0.4). My DWI data is multi-shell, with 1 b=0, 64 b=1500, and 64 b=3000 volumes (PhaseEncodingDirection = j).

#!/bin/bash
cd “/data/subjects”
ml mrtrix3/3.0.4
ml fsl/6.0.7.16
ml ants/2.5.3

for_each * : dwidenoise IN/dwi.mif IN/dwi_denoised.mif -noise IN/noise.mif

for_each * : mrdegibbs IN/dwi_denoised.mif IN/dwi_denoised_unringed.mif -axes 0,1

for_each * : dwifslpreproc IN/dwi_denoised_unringed.mif IN/dwi_denoised_unringed_preproc.mif -rpe_none -pe_dir j -eddy_options " --repol --cnr_maps --slm=linear" -eddyqc_all eddyQC

for_each * : dwibiascorrect ants IN/dwi_denoised_unringed_preproc.mif IN/dwi_denoised_unringed_preproc_unbiased.mif -bias IN/bias.mif

for_each * : dwi2mask IN/dwi_denoised_unringed_preproc_unbiased.mif IN/dwi_mask_unbiased.mif

For most subjects, the dwi_mask_unbiased.mif was correctly generated. However, in 9 subjects, dwi2mask produces a completely white mask (i.e., the entire field of view is white instead of a brain-shaped mask).

Do you have any suggestions to improve the dwi2mask output in those cases?

Interestingly, in those 9 cases, dwifslpreproc creates a more accurate mask (eddy_mask.nii.gz) that appears to correctly segment the brain (but sometimes with holes).

Would it be appropriate to use eddy_mask.nii.gz as a replacement in these cases? If so, are there any references or best practices that support this?

Any advice is appreciated.

Thanks!

p.s. The following image is the dwi_denoised_unringed_preproc_unbiased.mif of the above masks:

[WilliamFCB]

Hi Javier,
I typically use QSIprep for the DWI processing. I am not an expert in the MRtrix3 tools (although I use them in e.g., fixel analysis). Anyway, for brainmasks, I typically use SynthStrip (synthstrip.io). It is part of Freesurfer (mri_synthstrip). I successfully used it for different MRI modalities. Maybe check it out. Of course, you need to investigate what might explain the 9 failed and critically check the quality of the others, but it seems you did the latter.

Hope this helps
Cheers
William

[Javier]

Hello William,

Thank you for your advice! I actually tested using SynthStrip in Neurodesk to generate brain masks for the DWI images, and so far, the results are much better than those obtained with dwi2mask. In fact, one of the nine problematic brain masks is now perfect.

I still need to wait for the processing of all images to finish, but so far, the outputs look great!

Thanks again!