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

Dear Jonathan, the munger script is fussy about the naming of your input images. The floating images (but not the template) must end in 01.nrrd 02.nrrd etc to denote the channel. See http://flybrain.mrc-lmb.cam.ac.uk/dokuwi... (linked from the Fiji CMTK gui GitHub page) for further details.

In terms of the munger command line switches

-c 01 is the default and can be omitted but
-r 02 will only reformat channel 2, whereas you probably want
-r 0102 so that you can check that the nc82 registration In channel 1 worked ok.

All the best, Greg.

Hi Greg,

Ok it seems I had the wrong image folder selected. I used -r 0102 and now have registered images for both channels.

Thank you!

Jonathan