# Tractography through ROIs from TMS-DICOM-Data - anyone experience?

**URL:** <https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502>\
**Category:** Support\
**Tags:** diffusion, tractography\
**Created:** [June 14, 2017, 3:43pm UTC](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502 "2017-06-14T15:43:35Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![LGG](https://avatars.discourse-cdn.com/v4/letter/l/ea666f/32.png) [@LGG](https://discourse.slicer.org/u/LGG)\
**Post date:** [June 14, 2017, 3:43pm UTC](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502/1 "2017-06-14T15:43:35Z")

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Hi everyone,

I would like to create ROIs out of DICOM-Data that has been acquired through TMS (with Slicer 4.6). The aim is to run tractography through these ROIs. I tried to do full brain tractography and use the TMS-Data as labelmaps, but so far I haven’t been able to produce a labelmap out of the TMS-Data. Does anyone have experience with that or an idea how to approach this? It would be a great help!

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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:** [June 14, 2017, 4:00pm UTC](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502/2 "2017-06-14T16:00:25Z")

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Hi Lioba,

Can you please describe in more detail the data, what you tried, and what the issue was? One or two screenshots might help. I have used TMS in the past, but it was a proprietary system and we only received lists of coordinates and amplitudes (not DICOM). If you receive a DICOM heatmap image of stimulation, for example, you will likely need to threshold it (using one of the editor tools) to produce a binary labelmap which could then be used as an input ROI.

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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:** [June 14, 2017, 4:01pm UTC](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502/3 "2017-06-14T16:01:01Z")

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(also, if you send screenshots or share data, **please make sure to crop any patient data!** )

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**Author:** ![LGG](https://avatars.discourse-cdn.com/v4/letter/l/ea666f/32.png) [@LGG](https://discourse.slicer.org/u/LGG)\
**Post date:** [June 14, 2017, 6:13pm UTC](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502/4 "2017-06-14T18:13:21Z")

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Hi Isaiah!

Thank you so much for that quick reply! Well my thought was to create a labelmap in the Editor, putting the TMS-points (its just several mapping-locations without any brain tissue underneath - I took a screenshot of it) as a Master Volume to create a labelmap of it. But that didn’t work (screenshot No. 2). I actually don’t really understand what the software does when it creates a merge label map. I actually want it to accept all the TMS-points as ROIs, or all of them together as one ROI (which seems to be more probable to implement).

I would be so glad if there’s a solution for that!

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/a/ba038cdd4fcb37443d2a8b7e4781e8b87a9992b9.png)

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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:** [June 14, 2017, 7:37pm UTC](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502/5 "2017-06-14T19:37:26Z")

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It looks like the threshold is too low. Move the mouse cursor over the dots, then look at the value in the “Data Probe” area in the bottom-left side of the window. Then set the threshold to only include that value – the dots should be highlighted as the threshold is changed. Here is a video demonstrating usage of the threshold tool: