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Mar 4, 2019  04:03 PM | Lucy Heap
Running munger scripts on Ubuntu
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
Mar 4, 2019  06:03 PM | Greg Jefferis
RE: Running munger scripts on Ubuntu
Dear Lucy,

You can run these scripts by opening a Terminal window and doing 
sh /path/to/mungerscript.sh

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 
ls -l /path/to/mungerscript.sh

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:
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
Mar 5, 2019  08:03 AM | Greg Jefferis
RE: Running munger scripts on Ubuntu
Originally posted by Greg Jefferis:
Dear Lucy,

You can run these scripts by opening a Terminal window and doing 
sh /path/to/mungerscript.sh
As for why double clicking them does nothing 


See also e.g. https://askubuntu.com/questions/286621/h...