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  • QuickNII_EBRAINS.mp4

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1	1	== (% style="color:#c0392b" %)Video tutorial(%%) ==
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3		-== ==
	3	+== ==
4	4
5	5	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
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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]]
20	20
	21	+(% id="HQuickSTEPS:" %)
	22	+(((
21	21	== (% style="color:#c0392b" %)QuickSTEPS:(%%) ==
	24	+)))
22	22
23		-== Open //QuickNII// and load your images ==
	26	+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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25		-Open the //QuickNII// program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
26		-
27		-== **Anchoring procedure** ==
28		-
	28	+(% class="box infomessage" %)
	29	+(((
	30	+(% class="box infomessage" %)
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29	29	The alignment procedure consists of two main tasks:
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31	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.
	35	+1. Adjust the atlas slices generated along these angles to match individual section
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	37	+)))
33	33
34	34	=== A) To determine the cutting angles: ===
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45	45	Review the position of **all sections** in the series, adjust the width and height of atlas slices as necessary, **and save settings**.
46	46
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
	52	+**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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	54	+== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
49	49
50		-
	56	+**[[image:Collabs.quint.Image registration to reference atlas using QuickNII.WebHome@VisuAlign_illustration.png]]**
	57	+
	58	+ 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]].
	59	+
	60	+=== **The basic steps are the following:** ===
	61	+
	62	+1. Export your anchoring results from QuickNII in JSON format (click “Save JSON” in the Manage Data window). Save the file in the same folder as your image series.
	63	+1. Open VisuAlign by double-clicking on “VisuAlign.bat”, and load your image descriptor JSON (File -> Open).
	64	+1. Add markers for adjusting the non-linear alignment. Drag a marker to move the atlas borders around it. Start with the borders of the section, and then adjust internal landmarks to fine-tune the alignment between the section and the atlas. Keep the number of markers to a minimum.
	65	+1. You can toggle “outline mode” by pulling the opacity slider to the far right. A colour picker on the right side of the slider becomes active for changing the outline colour.
	66	+1. Enabling “Debug mode” from the View menu toggles the display of triangles representing the deformation field, and allows you to change the colour of the triangles.
	67	+1. Finally, use File -> Save As to save your fine-tuned alignment as a new JSON file.
	68	+1. There is also an “Export”function for generating .flat files for Nutil.

QuickNII_EBRAINS.mp4

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	1	+XWiki.puchades

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	1	+26.3 MB

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