Last modified by puchades on 2022/02/18 13:55
From version 6.1
edited by puchades
on 2020/03/24 19:04
Change comment: There is no comment for this version
To version 8.4
edited by puchades
on 2020/03/25 13:38
Change comment: There is no comment for this version

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1 -3. Image registration to reference atlas using QuickNII
1 +3. Image registration to reference atlas using QuickNII and VisuAlign
Content
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10 10  
11 11  Use the small program “FileBuilder.bat” provided with QuickNII. A new window will open, and ask for the folder where your images are located. Point to the correct folder, mark all image files, and click ok. **An XML file is generated**. **Always save this file in the same folder as the resized images.**
12 12  
13 -=== Open QuickNII and load your images ===
13 +== Open QuickNII and load your images ==
14 14  
15 15  Open the QuickNII program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
16 16  
17 -A detailled 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/]]
17 +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/]]
18 18  
19 19  >The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole serie as these should be consistent. Once found in a few sections, apply the same angles to the rest of the serie.
20 20  
21 +== **Anchoring procedure** ==
22 +
21 21  **The basic steps are:**
22 22  
23 23  - (% style="color:#000000" %)Open one image in the beginning of the series and use anatomical landmarks to find the approximate anteroposterior position of the section.     Select the atlas modality to be overlayed to the image (MRI, Atlas, etc..)
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34 34  
35 35  (% style="color:#000000" %)- Review all sections, adjust atlas borders and save.
36 36  
39 +== **Nonlinear adjustment with VisuAlign** ==
37 37  
41 +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]]
42 +
43 +**The basic steps are:**
44 +
45 +-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”).
46 +
47 +-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.
48 +
49 +-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
50 +
51 +NB: keep the number of markers to a minimum.
52 +
53 +-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.
54 +
55 +-“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).
56 +
57 +- Use the “Save As”  to save your deformations as a new JSON file.
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