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
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
QuickNII filebuilder does not list my images although the size is ok.
–> The filename pattern should be consistent and the section numbers should have the same number of digits (see naming convention).
How can I refine my QuickNII registration?
–> Please us VisuAlign https://visualign.readthedocs.io/en/latest/.
Where can I find information about the coordinates of my images?
–> Information can be found in this guide under “Coordinates”