FSL Mask Resampling

Software Support
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1

Hello,

I have a brain mask of dimensions 176x208x176 but my functional MRI data has dimensions 48x64x48. I wanna resample or change by brain mask so that it matches the dimensions of my functional data. I attach also the brain mask and the functional data visualized on FSLEYES.

Thank you!

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2

Hi @Ibai_Azpeitia_Loiti1, if the images are already aligned with each other, you can do this from within FSLeyes via the Tools → Resample to image menu option:

  1. Make sure the mask image is selected in the overlay list
  2. Open Tools → Resample to image
  3. Choose the fMRI image in the Resample to reference dropdown
  4. You’ll probably want to select Nearest neighbour interpolation if you want the result to be a binary mask

If the images aren’t aligned, you will need to calculate a registration between your fMRI data, and whatever space the mask is in. If this doesn’t make sense to you, I’d recommend spending a little time going through the FSL course practical on registration.