<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 <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](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation).


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