3D Slicer. John Muschelli and Vadim Zipunnikov. Department of Biostatistics. November 18, 2011
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1 3D Slicer John Muschelli and Vadim Zipunnikov Department of Biostatistics November 18, 2011 John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
2 What is Slicer x Mac, Linux, Windows 3D slicer gallery: SlicerWelcome is useful at the beginning John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
3 Step 1: Loading data Brain atlas atlas.img/hdr (Analyze) 91 labeled regions 1 medial front-orbital gyrus right 2 middle frontal gyrus right 3 lateral ventricle left 4 insula right 5 precentral gyrus right 6 lateral front-orbital gyrus right 7 cingulate region right 8 lateral ventricle right 9 medial frontal gyrus left 10 superior frontal gyrus right 11 globus palladus right 12 globus palladus left 14 putamen left 15 inferior frontal gyrus left 16 putamen right 17 frontal lobe WM right 19 angular gyrus right 23 subthalamic nucleus right 25 nucleus accumbens right 26 uncus right 27 cingulate region left 29 fornix left 30 frontal lobe WM left 32 precuneus right 33 subthalamic nucleus left 34 PLICICPL* 35 PLICICPR* 36 hippocampal formation right 37 inferior occipital gyrus left 38 superior occipital gyrus right 39 caudate nucleus left 41 supramarginal gyrus left 43 anterior limb of internal capsule left 45 occipital lobe WM right 50 middle frontal gyrus left 52 superior parietal lobule left 53 caudate nucleus right 54 cuneus left 56 precuneus left 57 parietal lobe WM left 59 temporal lobe WM right 60 supramarginal gyrus right 61 superior temporal gyrus left 62 uncus left 63 middle occipital gyrus right 64 middle temporal gyrus left 69 lingual gyrus left 70 superior frontal gyrus left 72 nucleus accumbens left 73 occipital lobe WM left 74 postcentral gyrus left 75 inferior frontal gyrus right 80 precentral gyrus left 83 temporal lobe WM left 85 medial front-orbital gyrus left 86 perirhinal cortex right 88 superior parietal lobule right 90 lateral front-orbital gyrus left 92 perirhinal cortex left 94 inferior temporal gyrus left 95 temporal pole left 96 entorhinal cortex left 97 inferior occipital gyrus right 98 superior occipital gyrus left 99 lateral occipitotemporal gyrus right 100 entorhinal cortex right 101 hippocampal formation left 102 thalamus left 105 parietal lobe WM right 108 insula left 110 postcentral gyrus right 112 lingual gyrus right 114 medial frontal gyrus right 118 amygdala left 119 medial occipitotemporal gyrus left 128 anterior limb of internal capsule right 130 middle temporal gyrus right 132 occipital pole right 133 corpus callosum 139 amygdala right 140 inferior temporal gyrus right 145 superior temporal gyrus right 154 middle occipital gyrus left 159 angular gyrus left 165 medial occipitotemporal gyrus right 175 cuneus right 196 lateral occipitotemporal gyrus left 203 thalamus right 243 background 251 occipital pole left 254 fornix right 255 subarachnoid cerebro-spinal fluid John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
4 Step 1: Loading data File Add Data choose atlas.hdr (check Centered if applicable) Click Apply. note:.img files always go with.hdr, at this step.hdr should be chosen. Result: the data is loaded and you can see it in the three windows (directional) John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
5 Step 1: Loading data John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
6 Step 1: Loading data John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
7 Step 1: Loading data John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
8 Step 2: Creating Volume Volumes module choose volume name: atlas Apply Result: the volume created John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
9 Step 2: Creating Volume John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
10 Step 3: Creating Models Editor module choose Master Volume (depends on Slicer version) in Edit Selected Label Map window choose Level number and color click Threshold choose range (on the right you can see what areas are within this range) click Apply click MakeModel choose Name check Smooth Model (if applicable) Result: The model is built with the pre-chosen color. John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
11 Step 3: Creating Models The first model is corpus callosum labeled 133 (Threshold: 133:133), color: blue The second model is frontal lobe WM right labeled 17 (Threshold: 17:17), color: green The third model is frontal lobe WM left labeled 30 (Threshold: 30:30), color: red The last model is the whole brain (Threshold: 1:255), color: grey John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
12 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
13 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
14 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
15 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
16 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
17 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
18 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
19 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
20 Step 3: Creating Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
21 Step 4: Playing with the Models Models module shows the created models you can change visibility, opacity, set new color(in a much more convenient way), play with other things The brain opacity can be set to see the other regions John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
22 Step 4: Playing with the Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
23 Step 4: Playing with the Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
24 Step 4: Playing with the Models John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
25 Step 5: Saving the Scene Save Select scene (.mrml) and the volumes(.vtk) included into the scene Once the scene is saved you can load it later John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
26 Step 5: Saving the Scene John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
27 What is Slicer Awesome, duh. John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
28 Getting Data in Bring in data DICOM/Analyze/NIFTI : File Add Volume NIFTI : File Add Data You can bring in Analyze with Add Data if selecting.hdr file Generally need a brain image (structural / functional / template) - needs to be in same space as labels This makes up a scene (pretty much a project) John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
29 Labels Label map is surprisingly a map of labels. We ll be looking at categorical labels (thresholded or different structures) We need to construct a model, which essentially is a 3D construction of the data. We go to Editor Module (upper left of panel, around 10 o clock) John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
30 Labels: Structures Go to Editor Module (upper left of panel, around 10 o clock) Select the label map image in the data A pop-up dialog will ask you what label map (let s just try generic colors - which are not that good, but defaul) Click structures (if not expanded) Add Structures and pick a color Go to Threshold button (Picture) Provide a range: if categorical, just make range 1 to 1 if label is coded as 1, for example John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
31 Labels: Make some models Once you re done adding all your structures, then let s build the model! Merge all Merge and Build: there should be an image now in the 3D viewer. John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
32 Zombie it up: give me brains! Modules (where Editor is) Surface models Grayscale Model Maker Select New Model, brain image (not the label), defaults, and then run (at the bottom). Mmm Brains It s so dark!?!#$# John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
33 Tweak me Modules (where Editor is) Models Grayscale Model (Scroll down) Change opacity/diffusion Try some presets, they are the shades spheres (come on, try it). Bottom left corner - click the axes for different views Click the eye to take off / put on axes and such Click two check boxes to see things spin! John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
34 Feeling Saucy? Record movie gtk-recordmydesktop for Linux Jing for Mac Windows? - google John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
35 More applications: BOO Slicer can read in 4D data, but I haven t explored. bioimagesuite - if trying to record a 4D movie, this does it Originally for Cardiac 4D movies - so pretty good. If you find something better, tell me! John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
36 Other visualization tools: Most of the existing visualization tools are collected at: VisIt open source, scalable to petascale visual data analysis. VTK - Visualization ToolKit: 3D Slicer, VisIt, ParaView. Visualized is a sectional view of the rupturing of a steel container that is filled with a plastic bonded explosive and heated by a fire. copyright: VACET presentation John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
37 Other visualization tools: VisIt copyright: VACET presentation John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
38 Other visualization tools: VisIt copyright: VisIt manual John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
39 Other visualization tools: ParaView open source copyright: John Muschelli and Vadim Zipunnikov (JHU) 3D-Slicer November 18, / 39
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