TITLE: QuickNII Brain Atlas Registration
AUTHORS: Michael X. Henderson

[DESCRIPTION]
This protocol describes QuickNII brain atlas registration.

[STEPS]
SECTION: QuickNII Brain Atlas Registration
1. Open the QuickNII program folder.
SECTION: QuickNII Brain Atlas Registration
2. Open Filebuilder.  (FileBuilder loads your registration images by default settings without automated aligment, Skip to step 6 if using DeepSlice).
SECTION: QuickNII Brain Atlas Registration
3. Navigate to the QVN folder with the brain image exports from QuPath.
SECTION: QuickNII Brain Atlas Registration
4. Click all images to be registered, and click “Open”. 
 

SECTION: QuickNII Brain Atlas Registration
5. Press “SAVE XML”. Navigate to the QVN folder and save as "Filebuilder XML". Close FileBuilder.
SECTION: QuickNII Brain Atlas Registration
6. Open the application QuickNII. Press “Manage Data” > “Load” and load the XML file that was just generated in step 5.  (DeepSlice: load results.XML from QVN folder).
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7. Double click on the first image, and it will show up on the Atlas in QuickNII.


 

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8. Open Rainbow 2017 atlas in upper left hand corner (1).
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9. You can see the overlay better by dragging the transparency bar (2)
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10. For first section, find anteroposterior position. To do this, drag the sagittal red dot (3) to the correct rostro-caudal position. Click “Store” to save the position.
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11. Repeat for the last section. This will bring all other sections to the approximately correct position.
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12. Adjust each individual section to the appropriate place in the atlas by adjusting. These may need to be done iteratively until the correct plane of section is identified. 
 
a. Rotation: clockwise or counter-clockwise (4).
b. Brain Size: in the x and y direction (5).
c. Rostro-caudal position: sagittal view.
d. Left-Right plane: Pull Horizontal view bar.
e. Front-back plane: Pull Sagittal view bar.
 

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13. Click “Store” before moving off section or it will not save!
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14. Navigate to next section by double clicking on it in the Manage Data window, or by clicking the < and > arrows in the upper right. Edit all sections as noted in step 12.
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15. Click “Manage Data”.
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16. Click “Export Propagation” and save this XML file as “QuickN XML.xml" within the QVN folder. 

 

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17. Click “Save JSON” and label it “QuickN JSON”. This JSON file is used for Visualign.
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18. For QMask, go back to the first section.
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19. Adjust the horizontal plane (Right) in the atlas to match hemispheric split. Ensure proper bisecting by confirming with in the coronal plane.
 
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20. Open QMask Coordinates Excel File.
SECTION: QuickNII Brain Atlas Registration
21. Hover the cursor over the brain viewing window and record x-y-z coordinates (shown in the top left of the window) for three parts of the brain: Top-Left, Top-Right, Bottom-Left. Record coordinates in the QMask Coordinates file.