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12	12	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
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14		-Before you get started with image registration, make sure your images are the right size, and files are named according to the QUINT naming convention. See [[2. Image pre-processing with Nutil Transform>>2. Image pre-processing with Nutil Transform]] for details.
	14	+Before you get started with image registration, make sure your images are the right size, and files are named according to the QUINT naming convention. See [[2. Image pre-processing with Nutil Transform>>doc:Collabs.quint.1\. Preparing the images.WebHome]] for details.
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16		-=== (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
	16	+=== (% style="color:#c0392b" %)Generate your image descriptor file with FileBuilder(%%) ===
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18		-(% style="color:#4e5f70" %)Use the small program “FileBuilder.bat” provided with //QuickNII//. A new window will open, and ask for the folder where your images are located. Point to the correct folder, mark all image files, and click ok. **An XML file is generated**. **Always save this file in the same folder as the resized images.**
	18	+(% style="color:#4e5f70" %)Use the small program “FileBuilder.bat” provided with //QuickNII//. A new window will open, and ask for the folder where your images are located. Point to the correct folder, mark all image files, and click OK. **An XML file is generated**. **Always save this file in the same folder as the resized images.**
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20	20	== (% style="color:#c0392b" %)Open //QuickNII// and load your images(%%) ==
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24	24	A detailed //QuickNII// user manual as well as a demo dataset can be found on [[https:~~/~~/www.nitrc.org/projects/quicknii/>>https://www.nitrc.org/projects/quicknii/]]
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26		->(% style="color:#27ae60" %)The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole series as these should be consistent throughout. Once found in a few sections, apply the same angles to the rest of the series.
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28	28	== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
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30		-**The basic steps are:**
	28	+(% class="box infomessage" %)
	29	+(((
	30	+The alignment procedure consists of two main tasks:
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32		-(% 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..)
	32	+1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
	33	+1. Adjust the atlas slices generated along these angles to match individual sections.
	34	+)))
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34		--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.
	36	+=== (% style="color:#c0392b" %)A) To determine the cutting angles:(%%) ===
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36		--Save the positions for this section for now, they can be adjust later.
	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**. 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	+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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38		--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.
	45	+=== (% style="color:#c0392b" %)B) To fine-tune your alignment:(%%) ===
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40		--Explore a few sections in order to find the angles that fit most sections in order to achieve a global anchoring.
	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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42		--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.
	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.
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44		--Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.
45		-
46		--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//.
47		-
48	48	== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
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50	50	**[[image:VisuAlign_illustration.png]]**