MP2RAGE background removal in LEMON dataset

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random follow-up. for fun i translated that afni approach to antspy in case this is helpful to anyone:

import ants
uni = ants.image_read(“MP2RAGE_UNI_IMAGES.nii”)
inv2 = ants.image_read(“MP2RAGE_INV2.nii”)
inv2n4 = ants.n4_bias_field_correction(inv2)
max = inv2n4.max()
min = inv2n4.min()
inv2norm = (inv2n4-min) / (max-min)
bns = uni * inv2norm
ants.image_write(bns, “background_noise_suppressed.nii.gz”)

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LAYNII has a tool to remove the salt and pepper noise from MP2RAGE.

Here is a whole blog post about it:

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