<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">H Gabriel,<div class=""><br class=""></div><div class=""> I am glad you were able to get ChimeraX to work with the Oculus Rift to look at DICOM images. I think this could be a useful feature but it has a long ways to go. ChimeraX is primarily used for molecular visualization, electron microscopy, and 3d light microscopy. The DICOM medical imaging capabilities have had very little development. As you found out the "volume appearance" settings are almost all useless. That was a first try to borrow some image rendering settings from other software that is designed for medical imaging data, but as you saw it does not look good at all. The trouble is that the ChimeraX volumetric rendering is different than other medical imaging software and I have not had enough time to figure out the differences. I have not looked at Invesalius -- thanks for that suggestion.</div><div class=""><br class=""></div><div class=""> Although some of the volume appearance presets have the brightness curve as a horizontal line, they use different transparencies and colors along that horizontal line. Still I am not surprised that they don't work right. They probably should not have been added to ChimeraX because they are not working correctly.</div><div class=""><br class=""></div><div class=""> If you can figure out useful presets in Hounsfield units by manually adjusting the curve in ChimeraX Volume Viewer and setting colors for each node, I could add your specific presets to ChimeraX (and probably take out those old broken presets that were translated from other software). You can add vertices to the brightness curve on the histogram in Volume Viewer by right clicking and choosing menu entry "New Threshold". The color button above the histogram changes the color of the last vertex on the curve that you clicked on. This is easiest not using VR. If you get a useful setting you can use the command "volume settings #1" (if your DICOM model is #1) and it will report all the settings including "image levels" and "image colors" which describe the brightness curve. Those are the values I would need to add a volume appearance preset.</div><div class=""><br class=""></div><div class=""> Did you see this ChimeraX VR DICOM tutorial? Maybe it has some useful info for understanding the current limited capabilities.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/tutorials/dicom-vr.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/tutorials/dicom-vr.html</a></div><div class=""><br class=""></div><div class="">And this documentation page on ChimeraX DICOM page summarizes the features (not specific to VR).</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/dicom-quickref.html" class="">https://www.rbvi.ucsf.edu/chimerax/docs/user/dicom-quickref.html</a></div><div class=""><br class=""></div><div class=""> I agree with you that there is great potential for VR for medical imaging. It will take years of software improvement to make it work reasonably well, and since it is far from our primary audience for ChimeraX I cannot promise it will ever get those improvements.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 4, 2021, at 12:31 PM, Biomodelos 3D <<a href="mailto:unidadbiomodelos3d@gmail.com" class="">unidadbiomodelos3d@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Tom, thanks for your answer, I finally was able to use ChimeraX with Oculus Rift and it's absolutely amazing!. (I may have issues with some USB contacts in my notebook, don't know really).<div class="">My first concern is about DICOM images, as we produce Biomodels (VR, AR and 3D printed). I've been playing with ChimeraX Volume Viewer and Oculus. I found a lot of advantages to accelerate and improve our workflow for VR Biomodels and online demonstrations, I'd like to share:</div><div class="">-We can enter a VR environment immediately, no need of complex segmentation and post processing. This is really fast! and allows us to face emergency cases (usually our job can't face emergencies).</div><div class="">-We can directly measure in 3D and see those measures in real time.</div><div class="">-Doctors can have a much more realistic sense of the problem, in a much faster way, and relate it to different tissue densities.</div><div class="">-Working in VR over original dicom images, many dimensional errors are avoided (any segmentation process implies dimensional errors).<br class=""></div><div class="">-Also, interpretation errors (biomodelist's most important problems) are avoided, as doctors can see the study in VR by themselves, over an unaltered set of dicom images.</div><div class="">So I think ChimeraX VR capabilities are a complete game changer for doctors and surgeons.</div><div class=""><br class=""></div><div class="">Beside, I have some questions:</div><div class="">I created a .txt to load a <b class="">buttonpanel </b>having Volume Appearances Presets (file attached). It works really fine, but I noticed some issues:</div><div class=""><font color="#3d85c6" class=""><b class="">Black & White</b> does not work<br class=""><b class="">Glossy II and Glossy</b> have all points over an horizontal line<br class=""><b class="">High Contrast and Low Contrast</b> have no difference (and have all points over an horizontal line)<br class=""><b class="">Pencil </b>does not work<br class=""><b class="">Soft Skin II and Soft Skin III</b> are the same<br class=""><b class="">Soft on Blue and Soft on White</b> have no difference (and all points over an horizontal line)</font><br class=""><div class="">Appearances Presets look pretty different in ChimeraX compared to other Dicom Viewer software, can it be improved?</div><div class="">We use <b class="">Invesalius</b>, an open source brazilian software, as our mainstream workflow to produce volumetric renderings and .stl or .obj surfaces from dicom images. Unfortunately, it has no real time VR or AR tools. But is really good in Volumetric Rendering and segmentation of surfaces based in <b class="">Hounsfield </b>scale thresholds. So I wonder if some kind of knowledge-interchange may be useful for both developments? Please let me know if you think so.</div></div><div class=""><br class=""></div><div class="">Thanks again!</div><div class=""><br class=""></div><div class="">Gabriel Massano</div><div class="">Biomodelos 3D, Hospital de Ninos, Córdoba, Argentina</div><div class=""><a href="http://www.biomodelos3d.com.ar/" class="">www.biomodelos3d.com.ar</a></div><div class=""><ChimeraX Volume_Presets.txt></div></div></div></blockquote></div><br class=""></div></body></html>