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

<pre><code>fslstats &lt;input&gt; -V
</code></pre>

<p>where <code>&lt;input&gt;</code> is the path to your mask NIfTI file. The returned numbers will be the mask volume in voxels and mm^3.</p>

<h3>FSL install</h3>

<p>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 <a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation" rel="nofollow noreferrer">their wiki for instructions</a>.</p>

CC BY-SA 4.0
2019-09-03T22:40:48.677Z
2019-09-04T14:21:45.917Z
2019-09-04T14:21:45.917Z
SpinUp __ A Davis
<p>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?</p>

<neuroscience><neuroimaging><software>
Find volume of lesion mask
SpinUp __ A Davis
# Find volume of lesion mask

(Asked by: username_0 on 2019-09-03)

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?

**Tags:** neuroscience, neuroimaging, software


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## 1 answers

### Answer by username_0 on 2019-09-03. Score: 2 | Accepted answer

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  -V

where  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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