Last modified by puchades on 2022/02/18 13:55
From version 5.9
edited by puchades
on 2020/03/24 19:02
Change comment: There is no comment for this version
To version 8.3
edited by puchades
on 2020/03/25 13:29
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -3. Image registration to reference atlas using QuickNII
1 +3. Image registration to reference atlas using QuickNII and VisuAlign
Content
... ... @@ -10,14 +10,16 @@
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..)
... ... @@ -30,6 +30,14 @@
30 30  
31 31  (% style="color:#000000" %)- Explore a few sections in order to find the angles fitting most sections in order to achieve a global anchoring.
32 32  
33 -(% style="color:#000000" %)- By having the same angles in these two sections (i.e. ML=+1; DV= -4), QuickNII will apply them to all other sections located in between. The antero-posterior positions of all images are also estimated
35 +(% style="color:#000000" %)- By having the same angles in these two sections (i.e. ML=+1; DV= -4), QuickNII will apply them to all other sections located in between. The antero-posterior positions of all images are also estimated.
34 34  
37 +(% style="color:#000000" %)- Review all sections, adjust atlas borders and save.
35 35  
39 +== **Nonlinear adjustment with VisuAlign** ==
40 +
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 +-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”).
44 +
45 +Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII,