[Neuroimaging] Combining binary mask to 3D volume

[Jacob Bunyamin]

Good afternoon,

Apologies for this basic question,
If I wanted to create a new image from 3D volume and binary mask (combined
with multiplication), is it better to use np.asanyarray or np.multiply?

Thank you

Kind regards,

Jacob


On Tue, 14 Feb 2023 at 13:06, Jacob Bunyamin <jacob.bunyamin at monash.edu>
wrote:

> Thank you!
>
> On Tue, 14 Feb 2023 at 12:53, Christopher Markiewicz <
> markiewicz at stanford.edu> wrote:
>
>> Hi Jacob,
>>
>> If I'm understanding the problem correctly, you mean you have a 3D image
>> (maybe T1-weighted or similar) and a 3D binary mask, and what you would
>> like is the original image values where the mask is 1 and 0s where the mask
>> is 0.
>>
>> Assuming that's correct, I might take this approach:
>>
>> import nibabel as nib
>> import numpy as np
>>
>> img = nib.load(img_fname)
>> mask_img = nib.load(mask_fname)
>>
>> data = img.get_fdata()
>> mask = np.asanyarray(mask_img.dataobj) != 0
>>
>> # Remove data outside the mask
>> data[~mask] = 0
>>
>> masked_img = img.__class__(data, img.affine, img.header)
>> masked_img.to_filename(out_fname)
>>
>> I suspect nilearn has tools that would do this as well. And if your mask
>> is aligned to your original image but not have the same shape and affine,
>> you will need to resample your mask first before you can use the data
>> arrays in this way.
>>
>> Best,
>> Chris
>>
>> ________________________________________
>> From: Neuroimaging <neuroimaging-bounces+markiewicz=
>> stanford.edu at python.org> on behalf of Jacob Bunyamin via Neuroimaging <
>> neuroimaging at python.org>
>> Sent: Monday, February 13, 2023 19:50
>> To: neuroimaging at python.org
>> Cc: Jacob Bunyamin
>> Subject: [Neuroimaging] Combining binary mask to 3D volume
>>
>> Good afternoon,
>>
>> I am trying to overlay a binary mask to 3D volume and combine them into a
>> single file. Is there any way to do this?
>>
>> Thank you,
>>
>> Kind regards,
>>
>> Jacob
>>
>> --
>> Jacob Bunyamin
>> PhD Student
>>
>> Department of Neuroscience
>> Central Clinical School, Monash University
>> 99 Commercial Road
>> Melbourne VIC 3004
>> E: jacob.bunyamin at monash.edu<mailto:jacob.bunyamin at monash.edu>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>
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