Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -22,13 +22,11 @@
22	22
23	23	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)
24	24
25		-=== **Anchoring procedure** ===
	25	+(% class="box infomessage" %)
	26	+(((
	27	+**Anchoring procedure **The alignment procedure consists of two main tasks: 1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices. 2. Adjust the atlas slices generated along these angles to match individual sections.
	28	+)))
26	26
27		-The alignment procedure consists of two main tasks:
28		-
29		-1. Determine the dorsoventral and mediolateral cutting angle of the section series, apply same angles for all slices.
30		-1. Adjust the atlas slices generated along these angles to match individual sections.
31		-
32	32	=== A) To determine the cutting angles: ===
33	33
34	34	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.)
...	...	@@ -46,9 +46,9 @@
46	46
47	47	== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
48	48
49		-**[[image:VisuAlign_illustration.png]]**
	47	+**[[image:Collabs.quint.Image registration to reference atlas using QuickNII.WebHome@VisuAlign_illustration.png]]**
50	50
51		- A detailed //VisuAlign //user manual [[can be found here>>url:https://www.nitrc.org/docman/?group_id=1426]].
	49	+ 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]].
52	52
53	53	=== **The basic steps are the following:** ===
54	54
...	...	@@ -58,5 +58,4 @@
58	58	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.
59	59	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.
60	60	1. Finally, use File -> Save As to save your fine-tuned alignment as a new JSON file.
61		-
62		-
	59	+1. There is also an “Export”function for generating .flat files for Nutil.