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9	9	=== (% style="color:#000000" %)Generate your images descriptor file with FileBuider(%%) ===
10	10
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.**
	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	13	=== Open QuickNII and load your images ===
14	14
15		-Open the QuickNII program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
	15	+==== You can also add images ====
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	+[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
18	18
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.
	19	+Photo by David Clode
20	20
21		-**The basic steps are:**
	21	+==== Or code ====
22	22
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..)
	23	+Code blocks can be added by using the code macro:
24	24
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.
26		-
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		-
	25	+{{code language="python"}}
	26	+x = 1
	27	+if x == 1:
	28	+ # indented four spaces
	29	+ print("x is 1.")
	30	+{{/code}}