Thanks, I did glance through that User Guide but I don't think there are any sections in it that would help a non-coder. Here's how explicit I'm trying to make the instructions to align fly brains, below. I haven't been able to find any instructions for the CMTK interface in Fiji, since the link to the flybrain wiki is down. Haven't been able to get CMTK to work from Fiji, myself. Using the "Registration Parameter Preset" of the full brain and changing no other settings, the Log just says "Registration warp failed, Registration affine failed." So I currently only wrote pre-prep instructions:

Here's the type of thing I'm trying to write:
Follow the instructions at:
https://github.com/sandorbx/Parallel-Fij...
(This will require typing a few things into a command line but don't worry if you're not a coder, it will tell you what to do).
For the part that requires Ubuntu, note that it must be installed through the Microsoft Store, which can have problems if not recently updated through Windows Updates. Update, then reboot your computer.
When the instructions refer to the file named "Parallel_Fiji_CMTK_Registration***.ijm", that comes from a collection of files from the green "Code" button at the top of the instructions page. Download the ZIP then extract it, and move the relevant .ijm file for your operating system as outlined in the instructions.
If your confocal stack is not already separated out into different files for different channels, open it in Fiji. Scroll to a slice where you can see the brain.
>Image >Transform >Rotate >Check "Preview" >Change angle until brain is upright
Draw a box around brain but not too tightly
>Image >Crop
>Image >Color >Split channels
Select the nc82 reference channel image
>Save >NRRD >remove the leading characters that Fiji inserts, and give it a name ending in _01
Select the neuron stain image (e.g. GFP)
>Save >NRRD >choose exactly the same name as the reference image, but ending in _02
Check the FlyWire Gateway to see what template brains that site can work with, then download an appropriate one from:
https://www.janelia.org/open-science/jrc...
To run alignment in Fiji: >Plugins >Macros >Parallel Fiji CMTK Registration...