Hi all,

I'm working on registering an image stack to the JFRC2 brain. I am using the nc82 channel for registration, but would like to generate a NRRD file containing a different channel (channel 2). I tried adding the following (-c 01 -r 02) to register using the nc82 channel 1 and to reformat channel 2, but no reformatted NRRD volume is generated:

"/home/pogo/Desktop/Fiji.app/bin/cmtk/munger" -b "/usr/lib/cmtk/bin" -a -w -c 01 -r 02 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 4 -s "refbrain/JFRC2.nrrd" ss00731FixedSpacing

Please let me know if I'm approaching this correctly.


Sincerely,

Jonathan