# Viewing an FA image

**URL:** <https://discourse.slicer.org/t/viewing-an-fa-image/668>\
**Category:** Support\
**Tags:** diffusion\
**Created:** [July 11, 2017, 6:44pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668 "2017-07-11T18:44:22Z")\
**Posts on this page:** 10\
**Page:** 1

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**Author:** ![Rewati\_Kulkarni](https://avatars.discourse-cdn.com/v4/letter/r/8edcca/32.png) [@Rewati\_Kulkarni](https://discourse.slicer.org/u/Rewati_Kulkarni)\
**Post date:** [July 11, 2017, 6:44pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/1 "2017-07-11T18:44:22Z")

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Operating system: Mac OSX 10.9.5  
Slicer version: 4.7.0  
Expected behavior:  
Actual behavior:

I have a greyscale Fractional Anisotropy (FA) image, and I want to view it in RGB colour scheme, with white matter tract orientations too, if possible. I tried using the Volumes module, but the preset colour schemes only make the greyscale image look garish when colourful. I would like to view it the way the sample DTI downloaded from the 3D Slicer forum looks like, with a black background, and a 3D vector visualisation in RGB. Which module should I be using for this?

(I was able to load this FA image in another software and view it in 3d vector RGB visualisation, but I would really like to use Slicer over the other software).

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**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:** [July 11, 2017, 7:53pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/2 "2017-07-11T19:53:09Z")

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How does the other software (which one?) provide a directionally-coded visualization? There’s no directional information available in a grayscale FA, it’s a single scalar value per voxel.

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**Author:** ![Rewati\_Kulkarni](https://avatars.discourse-cdn.com/v4/letter/r/8edcca/32.png) [@Rewati\_Kulkarni](https://discourse.slicer.org/u/Rewati_Kulkarni)\
**Post date:** [July 12, 2017, 2:27pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/3 "2017-07-12T14:27:15Z")

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I am using FSL, and within that, FSLeyes to view the FA image. The image I  
have is actually called an FAV1 image, but when I checked online, I could  
not find a similar format listed anywhere.

_Rewati Kulkarni_

_Research Assistant, Injury Biomechanics Lab._

University of Pennsylvania,  
Department of Bioengineering  
_+1 267-648-7960_ | _[rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com) [rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com)_

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**Author:** ![Rewati\_Kulkarni](https://avatars.discourse-cdn.com/v4/letter/r/8edcca/32.png) [@Rewati\_Kulkarni](https://discourse.slicer.org/u/Rewati_Kulkarni)\
**Post date:** [July 12, 2017, 3:53pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/4 "2017-07-12T15:53:21Z")

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To explain better, I have attached the file I opened, and an image of what  
it looks like in FSL, when used with the 3D RGB vector visualisation  
option. I hope that makes what I am trying to say, clearer.

_Rewati Kulkarni_

_Research Assistant, Injury Biomechanics Lab._

University of Pennsylvania,  
Department of Bioengineering  
_+1 267-648-7960_ | _[rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com) [rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com)_

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**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:** [July 12, 2017, 4:03pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/5 "2017-07-12T16:03:08Z")

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Thanks - I don’t think attachment mail-in is supported (or the file may be too big). Please upload to something like dropbox/google drive/etc. and share the link.

However, based on [this document](https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/blob/master/userdoc/overlays.rst#vector) it sounds like they are storing components. I’m not sure if we have a way to visualize such an image in color right now.

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**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:** [July 12, 2017, 4:04pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/6 "2017-07-12T16:04:54Z")

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Might be possible to glyph it using: [http://apidocs.slicer.org/master/classvtkMRMLVectorVolumeDisplayNode.html](http://apidocs.slicer.org/master/classvtkMRMLVectorVolumeDisplayNode.html)

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<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:** [July 12, 2017, 4:19pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/7 "2017-07-12T16:19:01Z")

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Please note – if you share data, it must be anonymized (no identifiable information in the image, metadata, or even filename).

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<div class="post-metadata">

**Author:** ![Rewati\_Kulkarni](https://avatars.discourse-cdn.com/v4/letter/r/8edcca/32.png) [@Rewati\_Kulkarni](https://discourse.slicer.org/u/Rewati_Kulkarni)\
**Post date:** [July 12, 2017, 4:20pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/8 "2017-07-12T16:20:07Z")

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I’ve attached the google drive link to the files I tried to send earlier:

[https://drive.google.com/drive/folders/0B9ZRwZrndb2DYXl0LVpZcHdzYmc?usp=sharing](https://drive.google.com/drive/folders/0B9ZRwZrndb2DYXl0LVpZcHdzYmc?usp=sharing)

_Rewati Kulkarni_

_Research Assistant, Injury Biomechanics Lab._

University of Pennsylvania,  
Department of Bioengineering  
_+1 267-648-7960_ | _[rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com) [rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com)_

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<div class="post-metadata">

**Author:** ![Rewati\_Kulkarni](https://avatars.discourse-cdn.com/v4/letter/r/8edcca/32.png) [@Rewati\_Kulkarni](https://discourse.slicer.org/u/Rewati_Kulkarni)\
**Post date:** [July 13, 2017, 12:51pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/9 "2017-07-13T12:51:12Z")

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Hello Isaiah, did you have a chance to go over the files I sent you?

_Rewati Kulkarni_

_Research Assistant, Injury Biomechanics Lab._

University of Pennsylvania,  
Department of Bioengineering  
_+1 267-648-7960_ | _[rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com) [rewati.p.k01@gmail.com](mailto:rewati.p.k01@gmail.com)_

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<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:** [July 14, 2017, 5:12pm UTC](https://discourse.slicer.org/t/viewing-an-fa-image/668/10 "2017-07-14T17:12:08Z")

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I took a look at the file, but I’m still unsure about the conventions it uses (what is the order of the image components, etc.). As of now we don’t have a way to display such a file.