Attention: The EBRAINS IAM will be down Monday, the 21st July 2025, from 17.00 CEST (my timezone) for up to 1 hour. This will any affect services requiring an EBRAINS login, we apologise for any inconvenience caused.


Changes for page Widget 3D Head

Last modified by paulapopa on 2025/05/30 15:03
From version 24.1
edited by paulapopa
on 2023/03/24 07:58
Change comment: There is no comment for this version
To version 29.1
edited by paulapopa
on 2025/05/30 14:55
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -9,14 +9,17 @@
9 9  It is a Jupyter widget intended for visualization of the 3D Head data available for a patient:
10 10  
11 11  * surfaces of different types (cortex, face, skull, etc)
12 -* connectivity region centers
12 +* connectivity region centers and edges
13 13  * sensors locations (SEEG, MEG, EEG)
14 14  
15 +On cortical surfaces, it can also display region parcellation. 
16 +
15 15  == Inputs ==
16 16  
17 17  It supports the above data in the form of their corresponding TVB datatypes:
18 18  
19 19  * Surface (CorticalSurface, FaceSurface, etc)
22 +* Parcellation (RegionMapping)
20 20  * Connectivity
21 21  * Sensors (SensorsInternal, SensorsMEG, SensorsEEG)
22 22  
... ... @@ -31,15 +31,12 @@
31 31  
32 32  We need to first import the widget __API from tvbwidgets__// //package, together with the __TVB API __and the __display__ function:
33 33  
34 -(% class="box" %)
35 -(((
37 +{{code language="python" layout="LINENUMBERS"}}
36 36  import tvbwidgets.api as api
37 -
38 38  from tvb.simulator.lab import *
40 +from IPython.core.display_functions import display 
41 +{{/code}}
39 39  
40 -from IPython.core.display_functions import display
41 -)))
42 -
43 43  Then, there are 2 options to work with the widget:
44 44  
45 45  1. Use a file browser to load the data and automatically display it
... ... @@ -47,86 +47,64 @@
47 47  
48 48  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:
49 49  
50 -(% class="box" %)
51 -(((
50 +{{code language="python" layout="LINENUMBERS"}}
52 52  widget = api.HeadBrowser()
53 53  display(widget)
54 -)))
53 +{{/code}}
55 55  
56 -{{html}}
57 -<iframe width="840" height="480" src="https://www.youtube.com/embed/BCCh-wdcnVo" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
58 -{{/html}}
59 59  
60 -
61 61  For the second option, the API is described below:
62 62  
63 -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:
64 64  
65 -(% class="box" %)
66 -(((
67 -widget = api.HeadWidget()
60 +{{code language="python" layout="LINENUMBERS"}}
61 +surface = surfaces.Surface.from_file()
62 +surface.configure()
68 68  
69 -face = surfaces.FaceSurface().from_file()
70 -
64 +face = surfaces.Surface.from_file('face_8614.zip')
71 71  face.configure()
72 72  
73 -widget.add_datatype(face)
74 -display(widget)
75 -)))
67 +reg_map = region_mapping.RegionMapping.from_file()
76 76  
77 -{{html}}
78 -<iframe width="840" height="480" src="https://www.youtube.com/embed/8bmjKp3BYFA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
79 -{{/html}}
80 -
81 -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.
82 -
83 -The **Config** object can be used to tweak the display options for each datatype.
84 -
85 -In the code below, we add a **Connectivity** and SEEG **Sensors:**
86 -
87 -(% class="box" %)
88 -(((
89 -conn = connectivity.Connectivity().from_file()
90 -
69 +conn = connectivity.Connectivity.from_file()
91 91  conn.configure()
92 92  
93 -widget.add_datatype(conn)
72 +seeg = sensors.SensorsInternal.from_file()
73 +seeg.configure()
74 +{{/code}}
94 94  
76 +Then we prepare the **HeadWidget** for display:
95 95  
96 -seeg = sensors.SensorsInternal().from_file()
78 +{{code language="python" layout="LINENUMBERS"}}
79 +widget = api.HeadWidget([face, conn, seeg])
80 +display(widget)
81 +{{/code}}
97 97  
98 -seeg.configure()
83 +[[image:head.png]]
99 99  
100 -widget.add_datatype(seeg, api.HeadWidgetConfig(name='SEEG'))
101 -)))
85 +Next, we can continue adding other datatypes to this widget, by calling //**add_datatype**// multiple times.
102 102  
103 -{{html}}
104 -<iframe width="840" height="480" src="https://www.youtube.com/embed/6UQhL9gd1HM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
105 -{{/html}}
87 +In the code below, we add the **CorticalSurface** with a **RegionMapping** as parcellation**:**
106 106  
107 -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}}
108 108  
109 -(% class="box" %)
110 -(((
111 -reg_map = region_mapping.RegionMapping.from_file()
93 +[[image:cort.png]]
112 112  
113 -config = api.HeadWidgetConfig(name='Cortex')
114 114  
115 -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:
116 116  
117 117  
118 -cortex = surfaces.CorticalSurface().from_file()
119 119  
120 -cortex.configure()
100 +I can rotate the surface and zoom in/out:
121 121  
102 +[[image:parcel.png]]
122 122  
123 -widget = api.HeadWidget()
104 +I could also make it transparent to visualize the connectivity centers and their edges:
124 124  
125 -widget.add_datatype(cortex, config)
106 +[[image:conncenters.png]]
126 126  
127 -display(widget)
128 -)))
108 +Also, I can hide the connectivity and display only the SEEG sensors:
129 129  
130 -{{html}}
131 -<iframe width="840" height="480" src="https://www.youtube.com/embed/aDC2TJm2NxM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
132 -{{/html}}
110 +[[image:seeg.png]]
conncenters.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +509.5 KB
Content
cort.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +308.8 KB
Content
head.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.reginafilange
Size
... ... @@ -1,0 +1,1 @@
1 +245.6 KB
Content
menu.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +241.0 KB
Content
mm.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +242.7 KB
Content
parcel.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +273.8 KB
Content
seeg.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.paulapopa
Size
... ... @@ -1,0 +1,1 @@
1 +415.0 KB
Content
Public

TVB Widgets