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9	9	=== (% style="color:#000000" %)Generate your images descriptor file with FileBuider(%%) ===
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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	+(% style="color:#7f8c8d" %)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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13	13	== Open QuickNII and load your images ==
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23	23	**The basic steps are:**
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25		-- (% 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..)
	25	+(% 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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27		-- **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.
	27	+(% style="color:#000000" %)- **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.
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29		-- Save the positions for this section for now, you can adjust these later.
	29	+(% style="color:#000000" %)- Save the positions for this section for now, you can adjust these later.
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31		-- 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.
	31	+(% style="color:#000000" %)- Open the next image, located at the other end of the serie 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.
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33	33	(% style="color:#000000" %)- Explore a few sections in order to find the angles fitting most sections in order to achieve a global anchoring.
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37	37	(% style="color:#000000" %)- Review all sections, adjust atlas borders and save.
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	39	+(% style="color:#000000" %)-Export custom atlas slices corresponding to your series by clicking on the **“export Slices”** button..flat files
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39	39	== **Nonlinear adjustment with VisuAlign** ==
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	43	+**[[image:VisuAlign_illustration.png]]**
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41	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]]
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43	43	**The basic steps are:**
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55	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).
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57	57	- Use the “Save As”  to save your deformations as a new JSON file.
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