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39	39	1. **Tilt the atlas** by adjusting the dorsoventral and mediolateral angles. **Move the transparency slider** back and forth to see how well the atlas fits the section. The size of the atlas slice can also be modified for a better fit.
40	40	1. Once you have a fairly good match, save the alignment settings for this section and move on with the anchoring procedure. The settings can be fine-tuned later.
41	41	1. Open another image, located at the **other end of the series**, 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 your settings.
42		-1. Explore a few sections throughout the series in order to and find the angles that fit most sections in order to achieve a **good global anchoring**. We recommend to keep the cutting angles consistent throughout the entire section series, unless two blocks were cut separately.
	42	+1. Explore a few sections throughout the series in order to and find the angles that fit most sections in order to achieve a **good global anchoring**. We recommend to keep the cutting angles consistent throughout the entire section series (i.e. ML=+1; DV= -4), unless two blocks were cut separately.
43	43	1. Once two or more sections are anchored at their approximate position within the brain, **QuickNII propagates** **the cutting angles** across the entire image series. The anteroposterior position of the images is also estimated based on the section numbering.
44	44
45	45	=== (% style="color:#c0392b" %)B) To fine-tune your alignment:(%%) ===
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46	46
47	47	Review the position of **all sections** in the series, adjust the width and height of atlas slices as necessary, **and save settings**.
48	48
	49	+**Done! **Now you can **export customised atlas maps** corresponding to your series by clicking on the “Export Slices” button. The exported .flat files are used for the quantification by using Nutil Quantifier.
49	49
50		--By having the same cutting angles set for two sections (i.e. ML=+1; DV= -4), //QuickNII// will apply them to all the sections located between them. The antero-posterior positions of all the images are also estimated based on the numbering.
51		-
52		--Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.
53		-
54		--Export customised atlas maps corresponding to your series by clicking on the **“export Slices”** button. The exported .flat files are used for the quantification by //Nutil Quantifier//.
55		-
56	56	== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
57	57
58	58	**[[image:VisuAlign_illustration.png]]**