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1		-3. Image registration to reference atlas using QuickNII and Visu
	1	+3. Image registration to reference atlas using QuickNII and VisuAlign

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15	15	Open the QuickNII program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
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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/]]
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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.
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35	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.
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37	37	(% style="color:#000000" %)- Review all sections, adjust atlas borders and save.
	38	+
	39	+== **Nonlinear adjustment with VisuAlign** ==
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	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	+-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”).
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	45	+Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII,