Dwi2mask is not working properly

Dear Users,

I am using dwi2mask command with some 7T data. Unfortunately It produces missing spots in the temporal lobe and I’ve tried different threshold values.

Please find the meanB0 image here:

I would be grateful if you can please take a look at it.

Thanks in advance


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Hi Davide
7T data (well EPI or T2 images) suffer from inhomogeneity particular in the temporal lobe.
Not sure there is much you can do about it?
You can try using a manual mask or a T1 derived mask? Or manually edit the mask?
I don’t think N4 Bias Correction will be able to overcome these inhomogeneities, they are just too strong.

Hi Dave,

You could try out synthstrip-singularity (SynthStrip)
I started using it in different pipelines to create more optimal masks.
I tried it on your image.

mrconvert meanb0.mif mean.nii.gz
synthstrip-singularity -i meanb0.nii.gz -m meanb0_mask-b_0.nii.gz -b 0. (red mask in attached figure)
synthstrip-singularity -i meanb0.nii.gz -m meanb0_mask-b_0_no-csf.nii.gz -b 0 --no-csf (blue in attached figure)
The overlap between the two masks is in purple. Seems that combining them might give you a good starting point