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15	15	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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17		-A detailled 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/]]
	17	+The QuickNII user manual is found on [[https:~~/~~/www.nitrc.org/docman/?group_id=1341.>>https://www.nitrc.org/docman/?group_id=1341]]
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19		->The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole serie as these should be consistent. Once found in a few sections, apply the same angles to the rest of the serie.
	19	+>The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole serie. Once found, apply the same angles to the whole serie.
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21	21	**The basic steps are:**
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23	23	- (% 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 to the image (MRI, Atlas, etc..)
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25		-- **The transparency slider** can be used 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.
	25	+- **The transparency slider** can be used continuously to determine how well the atlas fits the section. Determine the sectioning angles (dorso-ventral and medio-lateral) by tilting the atlas.
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27		-- Save the positions for this section for now, you can adjust these later.
	27	+- Save the positions for this section. You can adjust these later
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29		-- Open the next image, located at the other end of the serie and repeat the same procedure as above i.e. (% style="color:#000000" %)find the approximate anteroposterior position of the section and test how well the cutting angles fit this section. Save the positions.
	29	+- Open the next image,
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31		-(% style="color:#000000" %)- Explore a few sections in order to find the angles fitting most sections in order to achieve a global anchoring.
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33		-(% style="color:#000000" %)- By having the same angles in these two sections (i.e. ML=+1; DV= -4), QuickNII will apply them to all other sections located in between. The antero-posterior positions of all images are also estimated
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