Hello, I'm interested in using a custom atlas in QuickNII. I ran the script from https://github.com/HumanBrainProject/Qui... (found at the bottom of https://www.nitrc.org/plugins/mwiki/inde...) to create my own .cutlas file.

Where should I place this file so that it I can load it in QuickNII? I've tried placing it in ~/QuickNII-ABAMouse-v3-2017.app/Contents/Resources, since I saw ABA_Mouse_CCFv3_2017_25um.cutlas in this directory, but it's not showing up in the drop-down atlas menu.

Any help would be appreciated!

Hi,

I don't have the Mac version of QuickNII in front of me, but somewhere inside there's a file called pack.txt (most probably it's at the exact same location where you found ABA_Mouse_CCFv3_2017_25um.cutlas), it contains the name of the cutlas file QuickNII will attempt to load. It contains the filename only, not even a line break after it.

I hope this helps, best regards,

Gergely

Hi Gergely, 

Thanks for the info! I'm getting this error, even though I confirmed the file is in the expected location: 
"STDERR:Exception in thread "main" java.io.FileNotFoundException: /Applications/QuickNII-ABAMouse-v3-2017.app/Contents/Resources/CCFv3_2020_10um.cutlas
 (No such file or directory)"

I also tried changing pack.txt back to "ABA_Mouse_CCFv3_2017_25um.cutlas" and it returned the same file not found error.

Hi,

This likely means that the text editor put some extra character(s) in the file. Possibly a line break at the end. Trying with a source code editor may help, perhaps.

Best regards,

Gergely