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1		-(% class="box infomessage" %)
2		-(((
3		-The alignment procedure consists of two main tasks:
	1	+== (% style="color:#c0392b" %)Video tutorial(%%) ==
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5		-~1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
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7		-2. Adjust the atlas slices generated along these angles to match individual section
8		-)))
	4	+(% style="color:#c0392b" %)[[image:QuickNII_EBRAINS.mp4||height="211" width="211"]]
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	8	+
	9	+== ==
	10	+
10	10	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
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12	12	Before you get started with image registration, make sure your images are the right size. Images should be in 24-bit PNG or JPEG format, with a resolution up to 16 megapixels (e.g. 4000x4000 or 5000x3000 pixels).
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20	20	== (% style="color:#c0392b" %)Links to Manuals(%%) ==
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22		-The latest QuickNII manual can be found here: [[(% style="color:#27ae60" %)QuickNII_user_guide>>https://quicknii.readthedocs.io/en/latest/index.html]]
	23	+The latest QuickNII manual can be found here: [[(% style="color:#27ae60" %)QuickNII_user_guide>>https://www.nitrc.org/docman/?group_id=1341]]
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24		-The latest VisuAlign manual can be found here: [[(% style="color:#27ae60" %)VisuAlign_user_guide>>https://visualign.readthedocs.io/en/latest/]]
	25	+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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26	26	(% id="HQuickSTEPS:" %)
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31	31	Open the //QuickNII// program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file (or JSON file if you have one from before)
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	34	+(% class="box infomessage" %)
	35	+(((
	36	+(% class="box infomessage" %)
	37	+(((
	38	+The alignment procedure consists of two main tasks:
	39	+
	40	+1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
	41	+1. Adjust the atlas slices generated along these angles to match individual section
	42	+)))
	43	+)))
	44	+
33	33	=== A) To determine the cutting angles: ===
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35	35	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.)
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44	44	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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46		-**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 registration with VisuAlign.
	58	+**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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48	48	== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
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50	50	**[[image:Collabs.quint.Image registration to reference atlas using QuickNII.WebHome@VisuAlign_illustration.png]]**
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	64	+ A detailed //VisuAlign //user manual [[can be found here>>https://www.nitrc.org/docman/index.php?group_id=1426&selected_doc_group_id=5980&language_id=1#folder]].
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53	53	=== **The basic steps are the following:** ===
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