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Last modified by puchades on 2022/02/18 13:55
From version 17.1
edited by sharoncy
on 2020/03/28 14:55
Change comment: There is no comment for this version
To version 1.4
edited by puchades
on 2020/03/24 09:59
Change comment: There is no comment for this version

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1 -3. Image registration to reference atlas using QuickNII and VisuAlign
1 +3. Image registration to reference atlas using QuickNII
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1 -XWiki.sharoncy
1 +XWiki.puchades
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1 -== [[image:BICCN_QNII_figure.png]] ==
1 +== H2 Headings Will Appear in Table of Content ==
2 2  
3 -== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
4 4  
5 -(% class="wikigeneratedid" %)
6 -**//QuickNII//** enable the registeration of the brain section images to the reference atlas to generate atlas maps that are customised to match the cutting plane and proportions of the sections. The adjusted are done by linear transformation only to allow angles to be calculated.
4 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
7 7  
8 -(% class="wikigeneratedid" %)
9 -**//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
6 +>This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
10 10  
11 -(% class="wikigeneratedid" %)
12 -The** QUINT workflow** is compatible with the atlas map output of both //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
8 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
13 13  
14 -== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
10 +=== H3 Headings Will Appear In The Table of Content ===
15 15  
16 -Resize your raw 2D images to 24-bit PNG and JPEG. Images can be loaded up to the resolution of 16 megapixels (e.g.4000x4000 or 5000x3000 pixels), however QuickNII does not benefit from image resolutions exceeding the resolution of the monitor in use.
12 +==== You can also add images ====
17 17  
18 -(% style="color:#4e5f70" %)The resized files must follow the naming convention having an unique ID in the format: sXXX.., with XXX.. reflecting the serial order and spacing of the sections (e.g. s002, s006, s010 for every 4^^th^^ section starting with section 2).
14 +[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
19 19  
20 -=== (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
16 +Photo by David Clode
21 21  
22 -(% style="color:#4e5f70" %)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.**
18 +==== Or code ====
23 23  
24 -== (% style="color:#c0392b" %)Open //QuickNII// and load your images(%%) ==
20 +Code blocks can be added by using the code macro:
25 25  
26 -(% 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.
22 +{{code language="python"}}
23 +x = 1
24 +if x == 1:
25 + # indented four spaces
26 + print("x is 1.")
27 +{{/code}}
27 27  
28 -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/]]
29 -
30 ->(% style="color:#27ae60" %)The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole series as these should be consistent throughout. Once found in a few sections, apply the same angles to the rest of the series.
31 -
32 -== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
33 -
34 -**The basic steps are:**
35 -
36 -(% 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 on the image (MRI, Atlas, etc..)
37 -
38 --Use the** transparency slider** continuously to determine how well the atlas fits the section. Determine the sectioning angles (dorso-ventral and medio-lateral) by tilting the atlas and adjust the atlas borders.
39 -
40 --Save the positions for this section for now, they can be adjust later.
41 -
42 --Open another image, located at the other end of the series, and repeat the same procedure as above, i.e. find the approximate anteroposterior position of the section and test how well the cutting angles fit this section. Save the positions.
43 -
44 --Explore a few sections in order to find the angles that fit most sections in order to achieve a global anchoring.
45 -
46 --By having the same cutting angles set for two sections (i.e. ML=+1; DV= -4), //QuickNII// will apply them to all the sections located between them. The antero-posterior positions of all the images are also estimated based on the numbering.
47 -
48 --Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.
49 -
50 --Export customised atlas maps corresponding to your series by clicking on the **“export Slices”** button. The exported .flat files are used for the quantification by //Nutil Quantifier//.
51 -
52 -== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
53 -
54 -**[[image:VisuAlign_illustration.png]]**
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]]
57 -
58 -**The basic steps are:**
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”).
61 -
62 --Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
63 -
64 --Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
65 -
66 -NB: keep the number of markers to a minimum.
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.
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).
71 -
72 -- Use the “Save As”  to save your deformations as a new JSON file.
29 +(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
30 +
BICCN_QNII_figure.jpg
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