users > RE: No reformatted files produced from Fiji/CMTK registration
Dec 17, 2020  10:12 AM | Greg Jefferis
RE: No reformatted files produced from Fiji/CMTK registration
Dear Jonathan,

the arguments to munger are case sensitive. Therefore you need to add 
-l a

i.e. lower case l.

All the best,

Greg.
Originally posted by Jonathan Perdomo:
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

Threaded View

TitleAuthorDate
Zane Aldworth Jun 28, 2019
Greg Jefferis Jun 28, 2019
Zane Aldworth Jun 28, 2019
Greg Jefferis Jun 29, 2019
Zane Aldworth Jun 30, 2019
Greg Jefferis Jun 30, 2019
Jonathan Perdomo Dec 17, 2020
RE: No reformatted files produced from Fiji/CMTK registration
Greg Jefferis Dec 17, 2020
Jonathan Perdomo Dec 18, 2020