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