Last modified by puchades on 2022/02/18 13:55
From version 24.1
edited by evanhancock
on 2020/07/21 09:33
Change comment: There is no comment for this version
To version 22.1
edited by puchades
on 2020/04/07 16:20
Change comment: There is no comment for this version

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1 -XWiki.evanhancock
1 +XWiki.puchades
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21 21  
22 22  (% style="color:#4e5f70" %)Open the //QuickNII// program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
23 23  
24 -A detailed //QuickNII// user manual as well as a demo dataset [[can be found here>>https://www.nitrc.org/projects/quicknii/]].
24 +A detailed //QuickNII// user manual as well as a demo dataset can be found on [[https:~~/~~/www.nitrc.org/projects/quicknii/>>https://www.nitrc.org/projects/quicknii/]]
25 25  
26 26  == (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
27 27  
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52 52  
53 53  **[[image:VisuAlign_illustration.png]]**
54 54  
55 - A detailed //VisuAlign //user manual [[can be found here>>https://www.nitrc.org/docman/?group_id=1426]].
55 + 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 56  
57 -**The basic steps are the following:**
57 +**The basic steps are:**
58 58  
59 -1. Export your anchoring results from QuickNII in JSON format (click “Save JSON” in the Manage Data window). Save the file in the same folder as your image series.
60 -1. Open VisuAlign by double-clicking on “VisuAlign.bat”, and load your image descriptor JSON (File -> Open).
61 -1. Add markers for adjusting the non-linear alignment. Drag a marker to move the atlas borders around it. Start with the borders of the section, and then adjust internal landmarks to fine-tune the alignment between the section and the atlas. Keep the number of markers to a minimum.
62 -1. You can toggle “outline mode” by pulling the opacity slider to the far right. A colour picker on the right side of the slider becomes active for changing the outline colour.
63 -1. Enabling “Debug mode” from the View menu toggles the display of triangles representing the deformation field, and allows you to change the colour of the triangles.
64 -1. Finally, use File -> Save As to save your fine-tuned alignment as a new JSON file.
59 +-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 +
61 +-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
62 +
63 +-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
64 +
65 +NB: keep the number of markers to a minimum.
66 +
67 +-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 +
69 +-“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 +
71 +- Use the “Save As”  to save your deformations as a new JSON file.