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
Dave
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
cheers
William
