Hello, I have an anatomical VOI that I created using BrainVoyager and have exported to nii format. I would like to use this VOI as a mask. Can I use this file directly as a mask, or do I need to change it first? For example, if I want to use this VOI as a mask when fitting a glm: glm = FirstLeve…

Typically masks are binarized files (1s in the VOI and 0s outside). Also, the file should have the same dimensions as the other images in your pipeline. If this is already the case, great! If not, there are a few things we can do: Binarize : fslmaths has a -bin which should conveniently binarize th…

Hi Steven, thanks so much for your explanation and solution! I was wondering if there was also a way to do this using nibabel or nilearn?

[image] How can I binarize and threshold images in Nilearn? Straightforward question, but if I have a list of T maps loaded using the image tools in Nilearn, how can I binarize them (i.e., all values greater than 3 are set to 1, and all values less than 3 are…

Please check the image orientation and the alignment of the exported file. BV does not know the meaning of a header. Please check carefully the right / left orientation (radiologist vs neurologist). I did it the other way around and transformed Freesurfer label into BV VOIs.

Neurostars

Creating a mask

Steven April 13, 2021, 2:47pm 4

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