Last modified by puchades on 2022/02/18 13:55
From version 18.1
edited by puchades
on 2020/03/30 16:49
Change comment: Deleted image "BICCN_QNII_figure.jpg"
To version 15.1
edited by sharoncy
on 2020/03/28 14:52
Change comment: There is no comment for this version

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9 9  **//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
10 10  
11 11  (% class="wikigeneratedid" %)
12 -The** QUINT workflow** is compatible with the atlas map output of both //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
12 +**The QUINT workflow** is compatible with atlas map output of //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
13 13  
14 14  == (% style="color:#c0392b" %)Preparation of the image series(%%) ==
15 15  
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53 53  
54 54  **[[image:VisuAlign_illustration.png]]**
55 55  
56 - A detailed //VisuAlign //user manual can be found on [[https:~~/~~/www.nitrc.org/docman/?group_id=1426>>https://www.nitrc.org/docman/?group_id=1426]]
56 + A detailed VisuAlign user manual can be found on [[https:~~/~~/www.nitrc.org/docman/?group_id=1426>>https://www.nitrc.org/docman/?group_id=1426]]
57 57  
58 58  **The basic steps are:**
59 59  
60 --Use the same folder as //QuickNII// with your png images and series descriptor (XML file). You will need the JSON version of the descriptor (it is generated by //QuickNII// by clicking “Save JSON”).
60 +-Use same folder as QuickNII with your png images and series descriptor (xml file). You will need the JSON version of the descriptor (it is generated in QuickNII by clicking “Save JSON”).
61 61  
62 --Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
62 +-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.
63 63  
64 64  -Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
65 65  
66 66  NB: keep the number of markers to a minimum.
67 67  
68 --The outline mode is toggled by pulling the opacity slider to the far right (as seen in the screenshot). A color picker to the right of it becomes active for changing outline colour.
68 +-The outline mode is toggled by pulling the opacity slider to the far right (as seen in the screenshot). A color picker to the right of it becomes active for changing outline color.
69 69  
70 --“Debug mode” displays triangles representing the deformation field, it is enabled from the View menu (and also enables a colour picker for changing the colour of the triangles).
70 +-“Debug mode” displays triangles representing the deformation field, it is enabled from the View menu (and also enables a color picker for changing the color of the triangles).
71 71  
72 72  - Use the “Save As”  to save your deformations as a new JSON file.
BICCN_QNII_figure.jpg
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