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Last modified by puchades on 2022/02/18 13:55
From version 4.1
edited by puchades
on 2020/03/24 17:38
Change comment: Uploaded new attachment "BICCN_QNII_figure.png", version {1}
To version 5.9
edited by puchades
on 2020/03/24 19:02
Change comment: There is no comment for this version

Summary

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Content
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1 -== ==
1 +== [[image:BICCN_QNII_figure.png]] ==
2 2  
3 3  == Preparation of the image serie ==
4 4  
5 +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.
5 5  
7 +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).
6 6  
7 -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.
9 +=== (% style="color:#000000" %)Generate your images descriptor file with FileBuider(%%) ===
8 8  
9 ->This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
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.**
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11 -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 +=== Open QuickNII and load your images ===
12 12  
13 -=== H3 Headings Will Appear In The Table of Content ===
15 +Open the QuickNII program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
14 14  
15 -==== You can also add images ====
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/]]
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17 -[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
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.
18 18  
19 -Photo by David Clode
21 +**The basic steps are:**
20 20  
21 -==== Or code ====
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..)
22 22  
23 -Code blocks can be added by using the code macro:
25 +- **The transparency slider** can be used 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.
24 24  
25 -{{code language="python"}}
26 -x = 1
27 -if x == 1:
28 - # indented four spaces
29 - print("x is 1.")
30 -{{/code}}
27 +- Save the positions for this section for now, you can adjust these later.
28 +
29 +- Open the next image, located at the other end of the serie and repeat the same procedure as above i.e. (% style="color:#000000" %)find the approximate anteroposterior position of the section and test how well the cutting angles fit this section. Save the positions.
30 +
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 +
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
34 +
35 +