Hi Greg,

I am having this same issue with just deselecting warping in the script generator but have not been able to run it with the included command you suggested (-L a). The command does not appear to be recognized. Am I calling it correctly?
My settings are:

Registration actions:
Affine
Reformat

Reformat Channels:
01

Registration Params:
Cachero, Ostrovsky 2010

Action
Write Script

(Further) Registration Params
-X 26 -C B -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -L a

Final script:
cd "/home/pogo/Desktop/JPerdomo MCFO_L320 Feb04 15min"
"/home/pogo/Desktop/Fiji.app/bin/cmtk/munger" -b "/usr/lib/cmtk/bin" -a -w -r 01 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -L a -T 4 -s "refbrain/JPerdomo-JFRC2.nrrd" images/JPerdomo-Feb04_Stack_01.nrrd

Error (this goes away when I remove -L a):
Unable to read reference brain


Best,

Jonathan