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36	36	=== (% style="color:#c0392b" %)A) To determine the cutting angles:(%%) ===
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38		-(% 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	+1. Open an image in the beginning of the series, and use anatomical landmarks to find the approximate anteroposterior position of the section in the atlas. Select the atlas modality to be overlaid on the image (MRI, Atlas, etc.)
	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	+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	+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. Ideally, the cutting angles should be consistent throughout the entire section series.
	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.
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40		--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.
	45	+=== (% style="color:#c0392b" %)B) To fine-tune your alignment:(%%) ===
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42		--Save the positions for this section for now, they can be adjust later.
	47	+Review the position of **all sections** in the series, adjust the width and height of atlas slices as necessary, **and save settings**.
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44		--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 the positions.
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46		--Explore a few sections in order to find the angles that fit most sections in order to achieve a global anchoring.
47		-
48	48	-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.
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50	50	-Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.