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1	1	== [[image:BICCN_QNII_figure.png]] ==
2	2
3		-(% class="wikigeneratedid" %)
4		-== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
	3	+== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
5	5
6	6	(% class="wikigeneratedid" %)
7		-**//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.
	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.
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9	9	(% class="wikigeneratedid" %)
10	10	**//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
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36	36
37	37	(% 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..)
38	38
39		--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.
	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.
40	40
41	41	-Save the positions for this section for now, they can be adjust later.
42	42