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1	1	== [[image:BICCN_QNII_figure.png]] ==
2	2
3		-== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
	3	+(% class="wikigeneratedid" %)
	4	+== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
4	4
5	5	(% class="wikigeneratedid" %)
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.
	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.
7	7
8	8	(% class="wikigeneratedid" %)
9	9	**//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
10	10
11	11	(% class="wikigeneratedid" %)
12		-The** QUINT workflow** is compatible with the atlas map output of both //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
	13	+**The QUINT workflow** is compatible with atlas map output of //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
13	13
14	14	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
15	15
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35	35
36	36	(% 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..)
37	37
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.
	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.
39	39
40	40	-Save the positions for this section for now, they can be adjust later.
41	41
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53	53
54	54	**[[image:VisuAlign_illustration.png]]**
55	55
56		- 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]]
	57	+ 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]]
57	57
58	58	**The basic steps are:**
59	59
60		--Use the 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 by //QuickNII// by clicking “Save JSON”).
	61	+-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”).
61	61
62		--Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by //QuickNII//.
	63	+-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.
63	63
64	64	-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
65	65
66	66	NB: keep the number of markers to a minimum.
67	67
68		--The outline mode is toggled by pulling the opacity slider to the far right (as seen in the screenshot). A color picker to the right of it becomes active for changing outline colour.
	69	+-The outline mode is toggled by pulling the opacity slider to the far right (as seen in the screenshot). A color picker to the right of it becomes active for changing outline color.
69	69
70		--“Debug mode” displays triangles representing the deformation field, it is enabled from the View menu (and also enables a colour picker for changing the colour of the triangles).
	71	+-“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).
71	71
72	72	- Use the “Save As”  to save your deformations as a new JSON file.