Version 16.1 by sharoncy on 2020/03/28 14:53
Hide last authors
puchades 4.2 1 == [[image:BICCN_QNII_figure.png]] ==
sharoncy 1.1 2
sharoncy 15.1 3 == (% style="color:#c0392b" %)//QuickNII// and //VisuAlign//(%%) ==
sharoncy 14.1 4
5 (% class="wikigeneratedid" %)
sharoncy 15.1 6 **//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 to allow angles to be calculated.
sharoncy 14.1 7
8 (% class="wikigeneratedid" %)
9 **//VisuAlign//** enables manual adjustments of the //QuickNII// atlas maps by nonlinear transformation to better match the sections.
10
11 (% class="wikigeneratedid" %)
sharoncy 16.1 12 The** QUINT workflow** is compatible with the atlas map output of both //QuickNII// and //VisuAlign// (the //VisuAlign// step is optional).
sharoncy 14.1 13
sharoncy 13.1 14 == (% style="color:#c0392b" %)Preparation of the image series(%%) ==
sharoncy 1.1 15
puchades 4.4 16 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.
puchades 3.1 17
puchades 9.4 18 (% style="color:#4e5f70" %)The resized files must follow the naming convention having an unique ID in the format: sXXX.., with XXX.. reflecting the serial order and spacing of the sections (e.g. s002, s006, s010 for every 4^^th^^ section starting with section 2).
puchades 4.4 19
puchades 11.1 20 === (% style="color:#c0392b" %)Generate your images descriptor file with FileBuider(%%) ===
puchades 3.1 21
sharoncy 14.1 22 (% 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.**
sharoncy 1.1 23
sharoncy 14.1 24 == (% style="color:#c0392b" %)Open //QuickNII// and load your images(%%) ==
sharoncy 1.1 25
sharoncy 14.1 26 (% 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.
sharoncy 1.1 27
sharoncy 14.1 28 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/]]
puchades 5.4 29
sharoncy 14.1 30 >(% 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.
puchades 5.4 31
puchades 11.1 32 == (% style="color:#c0392b" %)**Anchoring procedure**(%%) ==
puchades 7.2 33
puchades 5.6 34 **The basic steps are:**
35
sharoncy 14.1 36 (% 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..)
puchades 5.4 37
sharoncy 15.1 38 -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.
puchades 5.4 39
sharoncy 14.1 40 -Save the positions for this section for now, they can be adjust later.
puchades 5.4 41
sharoncy 14.1 42 -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.
puchades 5.4 43
sharoncy 14.1 44 -Explore a few sections in order to find the angles that fit most sections in order to achieve a global anchoring.
puchades 5.6 45
sharoncy 14.1 46 -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.
puchades 5.7 47
sharoncy 14.1 48 -Review the atlas to section match for all the sections, adjusting the atlas borders as necessary, and save.
puchades 8.2 49
sharoncy 14.1 50 -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//.
puchades 9.3 51
puchades 11.1 52 == (% style="color:#c0392b" %)**Nonlinear adjustment with VisuAlign**(%%) ==
puchades 8.2 53
puchades 9.2 54 **[[image:VisuAlign_illustration.png]]**
55
sharoncy 14.1 56 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]]
puchades 8.2 57
puchades 8.4 58 **The basic steps are:**
59
puchades 8.2 60 -Use same folder as QuickNII with your png images and series descriptor (xml file). You will need the JSON version of the descriptor (it is generated in QuickNII by clicking “Save JSON”).
61
puchades 8.4 62 -Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.
63
64 -Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.
65
66 NB: keep the number of markers to a minimum.
67
68 -The outline mode is toggled by pulling the opacity slider to the far right (as seen in the screenshot). A color picker to the right of it becomes active for changing outline color.
69
70 -“Debug mode” displays triangles representing the deformation field, it is enabled from the View menu (and also enables a color picker for changing the color of the triangles).
71
72 - Use the “Save As”  to save your deformations as a new JSON file.