# Measuring thickness

**URL:** <https://discourse.slicer.org/t/measuring-thickness/1259>\
**Category:** Support\
**Created:** [October 21, 2017, 1:08pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259 "2017-10-21T13:08:33Z")\
**Posts on this page:** 9\
**Page:** 1

<div class="post-metadata">

**Author:** ![navid\_mosleminiya](https://avatars.discourse-cdn.com/v4/letter/n/dfb087/32.png) [@navid\_mosleminiya](https://discourse.slicer.org/u/navid_mosleminiya)\
**Post date:** [October 21, 2017, 1:08pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/1 "2017-10-21T13:08:33Z")

</div>

how can I measure thickness in every point of the object and report with a color map

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/d/bd5ce43f399bcd6380156e854df69af6e6c722ee.jpeg)  
like this photo?

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [October 23, 2017, 6:07pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/2 "2017-10-23T18:07:35Z")

</div>

If you have two models, one of the inner surface and one of the outer surface you could use this extension:

[https://www.slicer.org/wiki/Documentation/4.8/Extensions/ModelToModelDistance](https://www.slicer.org/wiki/Documentation/4.8/Extensions/ModelToModelDistance)

Or if you means specifically you want to measure cortical thickness from mri you could look into Freesurfer ([http://surfer.nmr.mgh.harvard.edu/](http://surfer.nmr.mgh.harvard.edu/))

---

<div class="post-metadata">

**Author:** ![navid\_mosleminiya](https://avatars.discourse-cdn.com/v4/letter/n/dfb087/32.png) [@navid\_mosleminiya](https://discourse.slicer.org/u/navid_mosleminiya)\
**Post date:** [October 25, 2017, 2:54pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/3 "2017-10-25T14:54:35Z")

</div>

I want to perform cortical thickness analysis on a closed surface, isn’t this possible in the slicer at all?

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [October 25, 2017, 3:25pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/4 "2017-10-25T15:25:07Z")

</div>

Can you be more specific about what you need and why freesurfer doesn’t already do it? Slicer does a lot of things but we try not to duplicate tools that already exist.

---

<div class="post-metadata">

**Author:** ![navid\_mosleminiya](https://avatars.discourse-cdn.com/v4/letter/n/dfb087/32.png) [@navid\_mosleminiya](https://discourse.slicer.org/u/navid_mosleminiya)\
**Post date:** [October 27, 2017, 5:53am UTC](https://discourse.slicer.org/t/measuring-thickness/1259/5 "2017-10-27T05:53:29Z")

</div>

I need to do thickness analyzing in slicer, freesurfer is only on mac and linux which I don’t have and also is huge(4.4-4.6GB) so I would rather to do this with slicer

---

<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [October 27, 2017, 12:25pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/6 "2017-10-27T12:25:53Z")

</div>

Sorry, I don’t think there’s any easy way to do that.

---

<div class="post-metadata">

**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [October 27, 2017, 2:09pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/7 "2017-10-27T14:09:12Z")

</div>

Options:

- run in a virtual machine (VirtualBox is free; I think VMWare Player or current equivalent is also still free and has better graphics performance)
- if you have up-to-date Windows 10, you may be able to run under Windows Subsystem for Linux; someone posted instructions here:

[http://nuclear-imaging.info/site\_content/2016/09/12/installing-running-freesurfer-windows-10/](http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/)

(the second option will probably be faster and use less memory, but will have somewhat lower i/o performance and possibly unknown bugs if you hit unsupported syscalls)

---

<div class="post-metadata">

**Author:** ![navid\_mosleminiya](https://avatars.discourse-cdn.com/v4/letter/n/dfb087/32.png) [@navid\_mosleminiya](https://discourse.slicer.org/u/navid_mosleminiya)\
**Post date:** [October 27, 2017, 5:01pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/8 "2017-10-27T17:01:03Z")

</div>

tnx can you help me how I can do this after the installation?

---

<div class="post-metadata">

**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [October 27, 2017, 5:22pm UTC](https://discourse.slicer.org/t/measuring-thickness/1259/9 "2017-10-27T17:22:59Z")

</div>

Please follow the FreeSurfer support instructions and contact them with further questions.

[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport)