Last modified by puchades on 2022/02/18 13:55
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... ... @@ -1,1 +1,1 @@ 1 -3. Image registration to reference atlas using QuickNII and VisuAlign1 +3. Image registration to reference atlas using QuickNII - Content
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... ... @@ -8,18 +8,16 @@ 8 8 9 9 === (% style="color:#000000" %)Generate your images descriptor file with FileBuider(%%) === 10 10 11 -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.**11 +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 -== Open QuickNII and load your images == 13 +=== Open QuickNII and load your images === 14 14 15 15 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 detailedQuickNII user manualaswell as a demo dataset can befound 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]] 18 18 19 ->The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole serie as these should be consist ent. Once found in a few sections, apply the same angles to therest of the serie.19 +>The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole serie as these should be consistant. Once found in a few sections, apply the same angles to the whole serie. 20 20 21 -== **Anchoring procedure** == 22 - 23 23 **The basic steps are:** 24 24 25 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..) ... ... @@ -32,30 +32,4 @@ 32 32 33 33 (% style="color:#000000" %)- Explore a few sections in order to find the angles fitting most sections in order to achieve a global anchoring. 34 34 35 -(% 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. 36 36 37 -(% style="color:#000000" %)- Review all sections, adjust atlas borders and save. 38 - 39 -== **Nonlinear adjustment with VisuAlign** == 40 - 41 -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]] 42 - 43 -**The basic steps are:** 44 - 45 --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”). 46 - 47 --Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII. 48 - 49 --Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks. 50 - 51 -NB: keep the number of markers to a minimum. 52 - 53 --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. 54 - 55 --“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). 56 - 57 -- Use the “Save As” to save your deformations as a new JSON file. 58 - 59 - 60 - 61 -