Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 21.1
edited by paulapopa
on 2023/03/01 17:12
Change comment: There is no comment for this version
To version 31.1
edited by paulapopa
on 2025/05/30 15:03
Change comment: There is no comment for this version

Summary

Details

Page properties
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1 1  Source code: [[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>https://github.com/the-virtual-brain/tvb-widgets]]
2 2  
3 -Immediate testing: [[https:~~/~~/lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20Widgets/REPO/tvb-widgets/notebooks/HeadWidget.ipynb]]
3 +This is part of a Pypi release: [[https:~~/~~/pypi.org/project/tvb-widgets/>>https://pypi.org/project/tvb-widgets/]]
4 4  
5 +//**tvb-widgets**// is also already installed in the official image released for EBRAINS lab, where you can test it directly.
6 +
5 5  == Purpose ==
6 6  
7 7  It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
8 8  
9 9  * surfaces of different types (cortex, face, skull, etc)
10 -* connectivity region centers
12 +* connectivity region centers and edges
11 11  * sensors locations (SEEG, MEG, EEG)
12 12  
15 +On cortical surfaces, it can also display region parcellation. 
16 +
13 13  == Inputs ==
14 14  
15 15  It supports the above data in the form of their corresponding TVB datatypes:
16 16  
17 17  * Surface (CorticalSurface, FaceSurface, etc)
22 +* Parcellation (RegionMapping)
18 18  * Connectivity
19 19  * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
20 20  
... ... @@ -29,103 +29,77 @@
29 29  
30 30  We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
31 31  
32 -(% class="box" %)
33 -(((
37 +{{code language="python" layout="LINENUMBERS"}}
34 34  import tvbwidgets.api as api
35 -
36 36  from tvb.simulator.lab import *
40 +from IPython.core.display_functions import display 
41 +{{/code}}
37 37  
38 -from IPython.core.display_functions import display
39 -)))
40 -
41 41  Then, there are 2 options to work with the widget:
42 42  
43 43  1. Use a file browser to load the data and automatically display it
44 44  1. Use directly the API to load the data and display it
45 45  
46 -
47 47  For the first option, you have to run the following 2 lines of code in a notebook cell and then just use the UI controls:
48 48  
49 -(% class="box" %)
50 -(((
50 +{{code language="python" layout="LINENUMBERS"}}
51 51  widget = api.HeadBrowser()
52 52  display(widget)
53 -)))
53 +{{/code}}
54 54  
55 -{{html}}
56 -<iframe src="https://drive.google.com/file/d/1lY3X5eqJfOLmkmHuBa2iq_Aas8mDPa1e/preview" width="840" height="480" allow="autoplay"></iframe>
57 -{{/html}}
58 58  
59 -
60 60  For the second option, the API is described below:
61 61  
62 -In a new cell, we instantiate the **HeadWidget** and a **FaceSurface** datatype that we want to visualize. Using the //**add_datatype**// method we add the surface to our widget and __display__ the widget:
58 +In a cell, we load the data using the TVB API:
63 63  
64 -(% class="box" %)
65 -(((
66 -widget = api.HeadWidget()
60 +{{code language="python" layout="LINENUMBERS"}}
61 +surface = surfaces.Surface.from_file()
62 +surface.configure()
67 67  
68 -face = surfaces.FaceSurface().from_file()
69 -
64 +face = surfaces.Surface.from_file('face_8614.zip')
70 70  face.configure()
71 71  
72 -widget.add_datatype(face)
73 -display(widget)
74 -)))
67 +reg_map = region_mapping.RegionMapping.from_file()
75 75  
76 -{{html}}
77 -<iframe src="https://drive.google.com/file/d/1Egp9Lk-HGMATc9em6Kw_jSHmybTD2vzM/preview" width="840" height="480" allow="autoplay"></iframe>
78 -{{/html}}
79 -
80 -Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times. A maximum of 10 datatypes are supported by this widget.
81 -
82 -The **Config** object can be used to tweak the display options for each datatype.
83 -
84 -In the code below, we add a **Connectivity** and SEEG **Sensors:**
85 -
86 -(% class="box" %)
87 -(((
88 -conn = connectivity.Connectivity().from_file()
89 -
69 +conn = connectivity.Connectivity.from_file()
90 90  conn.configure()
91 91  
92 -widget.add_datatype(conn)
72 +seeg = sensors.SensorsInternal.from_file()
73 +seeg.configure()
74 +{{/code}}
93 93  
76 +Then we prepare the **HeadWidget** for display:
94 94  
95 -seeg = sensors.SensorsInternal().from_file()
78 +{{code language="python" layout="LINENUMBERS"}}
79 +widget = api.HeadWidget([face, conn, seeg])
80 +display(widget)
81 +{{/code}}
96 96  
97 -seeg.configure()
83 +[[image:head.png]]
98 98  
99 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
100 -)))
85 +Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
101 101  
102 -{{html}}
103 -<iframe src="https://drive.google.com/file/d/1RLwts75Hh31LoPdWLK7QOM61KIsOabF1/preview" width="840" height="480" allow="autoplay"></iframe>
104 -{{/html}}
87 +In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
105 105  
106 -We can also provide a **RegionMapping** to be used as colormap for a surface:
89 +{{code language="python" layout="LINENUMBERS"}}
90 +widget.add_datatype(surface, reg_map)
91 +{{/code}}
107 107  
108 -(% class="box" %)
109 -(((
110 -reg_map = region_mapping.RegionMapping.from_file()
93 +[[image:cort.png]]
111 111  
112 -config = api.HeadWidgetConfig(name='Cortex')
113 113  
114 -config.add_region_mapping_as_cmap(reg_map)
96 +In the upper-right corner, a menu is displayed. This will allow us to control what we want to visualize. For example, I can hide the head in order to get a better view of the cortical surface:
115 115  
116 116  
117 -cortex = surfaces.CorticalSurface().from_file()
118 118  
119 -cortex.configure()
100 +I can rotate the surface and zoom in/out:
120 120  
102 +[[image:parcel.png]]
121 121  
122 -widget = api.HeadWidget()
104 +I could also make it transparent to visualize the connectivity centers and their edges, by moving the slider highlighted in red:
123 123  
124 -widget.add_datatype(cortex, config)
106 +[[image:transp.png]]
125 125  
126 -display(widget)
127 -)))
108 +Or, I can hide the connectivity and display only the SEEG sensors:
128 128  
129 -{{html}}
130 -<iframe src="https://drive.google.com/file/d/1zrbjdb8Y4V5rqg7Y7LDGlHHMS0RH8luz/preview" width="840" height="480" allow="autoplay"></iframe>
131 -{{/html}}
110 +[[image:seeg.png]]
conncenters.png
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TVB Widgets