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I have drawn a lesion mask using FSLeyes on a T1-weighted image for MS patients. Is there tool to get the lesion volume from the mask?

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Assuming your mask is in NIfTI format (nii or nii.gz extension), you can use the fslstats command line tool for that. Just type fslstats on the command line to see the help text for command syntax and arguments. For your specific case, you can use:

fslstats <input> -V

where <input> is the path to your mask NIfTI file. The returned numbers will be the mask volume in voxels and mm^3.

FSL install

Since you said you used FSLeyes to draw your mask, I'm assuming you have the full install of the FSL package as well. If not, see their wiki for instructions.

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