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19	19	The latest VisuAlign manual can be found here: [[(% style="color:#27ae60" %)VisuAlign_user_guide>>https://www.nitrc.org/docman/index.php?group_id=1426&selected_doc_group_id=5980&language_id=1#folder]]
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21	21	== (% style="color:#c0392b" %)QuickSTEPS:(%%) ==
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23		-== Open //QuickNII// and load your images ==
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25		-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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27		-== **Anchoring procedure** ==
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29		-The alignment procedure consists of two main tasks:
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31		-1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
32		-1. Adjust the atlas slices generated along these angles to match individual sections.
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34		-=== A) To determine the cutting angles: ===
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36		-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.)
37		-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.
38		-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.
39		-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.
40		-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.
41		-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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43		-=== B) To fine-tune your alignment: ===
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45		-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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47		-**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. "Save JSON" in order to continue to non-linear regsitration with VisuAlign
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