8. Frequently asked questions

  1. I am using QuickNII to register my 2D coronal brain images with retrograde tracing. I completed all required steps through the filebuilder, but when I input my file to be registered the images does not appear, only the reference you have appears. Can you help me with this?

–> Please place the xml file in the same folder as the jpeg images, this usually solves this issue. You can read about it here: https://quicknii.readthedocs.io/en/latest/imageprepro.html#generate-a-xml-descriptor-file

  1. I have an error with the QuickNII filebuilder that just shows a black screen and shuts down.

–> This can happen if you have spaces in the path where the QuickNII software is located. For Windows 10 users, the filebuilder can be modified and it is described here: https://www.nitrc.org/plugins/mwiki/index.php/quicknii:MainPage

  1. How can I refine my QuickNII registration?

–> Please us VisuAlign https://visualign.readthedocs.io/en/latest/.

  1. Where can I find information about the coordinates of my images?

–> Information can be found in this guide under “Coordinates”