Hi everyone,

I'm new to using CMTK on ubuntu (previously I have run it on mac, but this is no longer possible). I have the GUI installed correctly into fiji, and am able to create command scripts with what seem like the right contents - for example:

#!/bin/sh
# 2019-03-05_09.21.33
cd "/home/lucy/Pictures/yourregistrationfolder"
"/home/lucy/Desktop/Fiji.app/bin/cmtk/munger" -b "/home/lucy/Desktop/Fiji.app/bin/cmtk" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 2 -s "refbrain/f3_190228.nrrd" images

However when I try and run these munger scripts, all that happens is they are opened in the text editor... I'm not sure what I'm missing here and it's probably something very simple, so I apologize in advance if that's the case.

Any help would be greatly appreciated!

Lucy

Dear Lucy,

You can run these scripts by opening a Terminal window and doing 

As for why double clicking them does nothing 

1. you may need to make them executable (chmod ug+x /path/to/mungerscript.sh in the Terminal). If you do 


you should be able to see if the file is executable.

2. the file extension of the script should be ".sh". If it isn't that could cause a problem, so let me know.

Best,

Greg.
Originally posted by Lucy Heap:

Originally posted by Greg Jefferis:
See also e.g. https://askubuntu.com/questions/286621/h...