<p>I must say I am not an expert, but the following sources look helpful:</p>

<ul>
<li><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075065" rel="nofollow noreferrer">Gao <em>et al</em>. (2013)</a> write </li>
</ul>

<blockquote>
  <p>The voxel value in the resulting dataset represents the number of
  streamline samples passing through this voxel times the expected
  length of these samples. The probabilistic-tractography-derived DDM
  was generated by keeping the values of those voxels located at the WGM
  interface and setting the remaining voxels to zero. Again, the DDMs
  were rendered on the 3D WGM interface in DTI space.</p>
</blockquote>

<ul>
<li>The <strong><a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide" rel="nofollow noreferrer">FDT Userguide</a></strong> discusses tractography and PROBTRACKX in <a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Including_targets_for_tractography_-_rationale" rel="nofollow noreferrer"><strong>section 2.6.3</strong></a>;</li>
<li><a href="https://www.ncbi.nlm.nih.gov/pubmed/18619589" rel="nofollow noreferrer">Catani &amp; Thiebaut de Schotten (2008)</a> discuss how diffusion tensor imaging (DTI) tractography can be used to virtually dissect white matter pathways in the living human brain; </li>
<li><a href="https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/fdt2.pdf" rel="nofollow noreferrer">This presentation</a> contains a lot of references;</li>
<li><a href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;cc032134.1304" rel="nofollow noreferrer">Specialist fora like this one</a> may be of help.</li>
</ul>

<p><sub><strong>References</strong><br>
<strong>-</strong> <a href="https://www.ncbi.nlm.nih.gov/pubmed/18619589" rel="nofollow noreferrer">Catani &amp; Thiebaut de Schotten, <em>Cortex</em> (2008); <strong>44</strong>(8):1105-32</a><br>
<strong>-</strong> <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075065" rel="nofollow noreferrer">Gao <em>et al</em>., <em>PLoS ONE</em> (2013); <strong>8</strong>(10): <em>e75065</em></a></sub></p>

CC BY-SA 3.0
2017-08-21T19:19:16.643Z
2017-08-21T19:19:16.643Z
AliceD
<p>I currently have track files of diffusion tensor imaging (DTI) data generated from FSL's probtrackX tractography tool. What is the best software to visualize the streamlines from FSL in 3D? </p>

CC BY-SA 4.0
2019-09-09T23:14:18.580Z
It doesn't generate streamline object as far as I know. I think the best way to visualize them would be to take the fdt_paths.nii file and threshold appropriately. Those are the voxels that streamlines traverse through.
SabCo
CC BY-SA 4.0
2019-08-02T14:10:40.533Z
I encounter the same problem in visualizing the tractography generated by FSL. I wanna ask do you find an appropriate way to solve the problem. I will appreciate that if you can give me a hint about this. Thank you so much.
Shi
<computational-modeling><neuroimaging><fmri>
How can I visualize DTI tractography streamlines generated from FSL's probtrackX in 3D?
SabCo
# How can I visualize DTI tractography streamlines generated from FSL's probtrackX in 3D?

(Asked by: username_0 on 2017-08-17)

I currently have track files of diffusion tensor imaging (DTI) data generated from FSL's probtrackX tractography tool. What is the best software to visualize the streamlines from FSL in 3D?

**Tags:** computational-modeling, neuroimaging, fmri

> **Comments:**
> **username_1**: I encounter the same problem in visualizing the tractography generated by FSL. I wanna ask do you find an appropriate way to solve the problem. I will appreciate that if you can give me a hint about this. Thank you so much.  
> **username_0**: It doesn't generate streamline object as far as I know. I think the best way to visualize them would be to take the fdt_paths.nii file and threshold appropriately. Those are the voxels that streamlines traverse through.  

---

## 1 answers

### Answer by username_2 on 2017-08-21. Score: 2

I must say I am not an expert, but the following sources look helpful:

* [Gao *et al*. (2013)](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075065) write

> The voxel value in the resulting dataset represents the number of
> streamline samples passing through this voxel times the expected
> length of these samples. The probabilistic-tractography-derived DDM
> was generated by keeping the values of those voxels located at the WGM
> interface and setting the remaining voxels to zero. Again, the DDMs
> were rendered on the 3D WGM interface in DTI space.

* The **[FDT Userguide](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide)** discusses tractography and PROBTRACKX in [**section 2.6.3**](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Including_targets_for_tractography_-_rationale);
* [Catani & Thiebaut de Schotten (2008)](https://www.ncbi.nlm.nih.gov/pubmed/18619589) discuss how diffusion tensor imaging (DTI) tractography can be used to virtually dissect white matter pathways in the living human brain;
* [This presentation](https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/fdt2.pdf) contains a lot of references;
* [Specialist fora like this one](https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;cc032134.1304) may be of help.

**References**  
**-** [Catani & Thiebaut de Schotten, *Cortex* (2008); **44**(8):1105-32](https://www.ncbi.nlm.nih.gov/pubmed/18619589)  
**-** [Gao *et al*., *PLoS ONE* (2013); **8**(10): *e75065*](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075065)


---

