Summary

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

Details

Page properties

Content

...	...	@@ -1,5 +1,17 @@
1	1	== [[image:BICCN_QNII_figure.png]] ==
2	2
	3	+(% class="wikigeneratedid" %)
	4	+== (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
	5	+
	6	+(% class="wikigeneratedid" %)
	7	+**//QuickNII//** enable the registeration of the brain section images to the reference atlas to generate atlas maps that are customised to match the cutting plane and proportions of the sections. The adjusted are done by linear transformation only.
	8	+
	9	+(% class="wikigeneratedid" %)
	10	+**//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
	11	+
	12	+(% class="wikigeneratedid" %)
	13	+**The QUINT workflow** is compatible with atlas map output of //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
	14	+
3	3	== (% style="color:#c0392b" %)Preparation of the image series(%%) ==
4	4
5	5	Resize your raw 2D images to 24-bit PNG and JPEG. Images can be loaded up to the resolution of 16 megapixels (e.g.4000x4000 or 5000x3000 pixels), however QuickNII does not benefit from image resolutions exceeding the resolution of the monitor in use.
...	...	@@ -8,41 +8,41 @@
8	8
9	9	=== (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
10	10
11		-(% 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.**
	23	+(% 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.**
12	12
13		-== (% style="color:#c0392b" %)Open QuickNII and load your images(%%) ==
	25	+== (% style="color:#c0392b" %)Open //QuickNII// and load your images(%%) ==
14	14
15		-(% style="color:#4e5f70" %)Open the QuickNII program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
	27	+(% style="color:#4e5f70" %)Open the //QuickNII// program from the .exe file. Once the program opens, click the **Manage data button** and load your XML file.
16	16
17		-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/]]
	29	+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/]]
18	18
19		->(% style="color:#27ae60" %)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.
	31	+>(% 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.
20	20
21	21	== (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
22	22
23	23	**The basic steps are:**
24	24
25		-(% 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..)
	37	+(% 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..)
26	26
27		--**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.
	39	+-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.
28	28
29		--Save the positions for this section for now, you can adjust these later.
	41	+-Save the positions for this section for now, they can be adjust later.
30	30
31		--Open the next image, located at the other end of the serie 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.
	43	+-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.
32	32
33		--Explore a few sections in order to find the angles fitting most sections in order to achieve a global anchoring.
	45	+-Explore a few sections in order to find the angles that fit most sections in order to achieve a global anchoring.
34	34
35		--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.
	47	+-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.
36	36
37		--Review all sections, adjust atlas borders and save.
	49	+-Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.
38	38
39		--Export custom atlas slices corresponding to your series by clicking on the **“export Slices”** button. The exported .flat files are used for the quantification by Nutil Quantifier.
	51	+-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//.
40	40
41	41	== (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
42	42
43	43	**[[image:VisuAlign_illustration.png]]**
44	44
45		-A detailed VisuAlign user manual can be found on [[https:~~/~~/www.nitrc.org/docman/?group_id=1426>>https://www.nitrc.org/docman/?group_id=1426]]
	57	+ A detailed VisuAlign user manual can be found on [[https:~~/~~/www.nitrc.org/docman/?group_id=1426>>https://www.nitrc.org/docman/?group_id=1426]]
46	46
47	47	**The basic steps are:**
48	48