Using a probabilistic mask with nilearn's NiftiMasker function

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#1

Hi,

I’m trying to use nilearn’s NiftiMasker function to extract gray matter.

I’ve run into variable degrees of compatibility with a probabilistic mask. Masking to generate reports seems fine. But when I try to save the masked data, I get an error stating that the mask isn’t binary:

       nii_masker = NiftiMasker(mask_img=graymatter_mask, memory="nilearn_cache",
                         memory_level=2, reports=1, t_r=TR)
        
        nii_masker.fit(epi) # this is fine
        report = nii_masker.generate_report() # no problems with reports, masking appears reasonable

        epi_masked_2d = nii_masker.transform(epi) # here, nilearn complains that the mask isn't binary

Does anyone know of any workarounds, short of just binarizing the probabilistic mask?

As always, thanks for your help.

Krista

#2

Hi,
You probably want ot binarize the brain mask: My understanding is that you want to extract time courses from all voxels that have a certain level of grey matter density ?
binary_mask = nilearn.image.math_img('i1 > threshold', i1=my_probabilistic_mask)
where threshold is picked by you, as a number between 0 and 1 I guess.
Best,