Preparation of the image series

Before you get started with image registration, make sure your images are the right size. Images should be in 24-bit PNG or JPEG format, with a resolution up to 16 megapixels (e.g. 4000x4000 or 5000x3000 pixels).

All image files should be named according to the serial order. You can use  Image pre-processing with Nutil Transform in order to rename your files.

Generate your image descriptor file with FileBuilder

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.

Links to Manuals

The latest QuickNII manual can be found here: QuickNII_user_guide

The latest VisuAlign manual can be found here: VisuAlign_user_guide

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)

A) To determine the cutting angles:

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.)
2. Tilt the atlas by adjusting the dorsoventral and mediolateral angles. Move the transparency slider back and forth to see how well the atlas fits the section. The size of the atlas slice can also be modified for a better fit.
3. Once you have a fairly good match, save the alignment settings for this section and move on with the anchoring procedure. The settings can be fine-tuned later.
4. 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 your settings.
5. Explore a few sections throughout the series in order to and find the angles that fit most sections in order to achieve a good global anchoring. We recommend to keep the cutting angles consistent throughout the entire section series (i.e. ML=+1; DV= -4), unless two blocks were cut separately.
6. Once two or more sections are anchored at their approximate position within the brain, QuickNII propagates the cutting angles across the entire image series. The anteroposterior position of the images is also estimated based on the section numbering.

B) To fine-tune your alignment:

Review the position of all sections in the series, adjust the width and height of atlas slices as necessary, and save settings.

Done! Now you can 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 using Nutil Quantifier. "Save JSON" in order to continue to non-linear registration with VisuAlign.

Nonlinear adjustment with VisuAlign

The basic steps are the following:

1. Export your anchoring results from QuickNII in JSON format (click “Save JSON” in the Manage Data window). Save the file in the same folder as your image series.
2. Open VisuAlign by double-clicking on “VisuAlign.bat”, and load your image descriptor JSON (File -> Open).
3. Add markers for adjusting the non-linear alignment. Drag a marker to move the atlas borders around it. Start with the borders of the section, and then adjust internal landmarks to fine-tune the alignment between the section and the atlas. Keep the number of markers to a minimum.
4. 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.
5. 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.
6. Finally, use File -> Save As to save your fine-tuned alignment as a new JSON file.
7. There is also an “Export”function for generating .flat files for Nutil.