Hi Greg,

Thank you for your fast response. I am using Manjaro in a virtual box...

As you suggested I checked which files are missing:

ls refbrain/Ref20131120pt14pl2.nrrd I can find the refbrain

ls images/21OctSP8Fish1_01.nrrd I can find all the images

ls /home/sarah/Fiji.app/bin/cmtk/bin/registration I cannot find registration in the cmtk bin.


Maybe I mixed up the folder structure when I installed CMTK (not with Fiji). The folder structure currently looks like this:

/home/sarah/Fiji.app/bin/cmtk/

In the cmtk folder are four subfolders (bin, include, lib and share)

/home/sarah/Fiji.app/bin/cmtk/bin/ includes the cmtk and munger script.

There is a folder which is called Registration, however, it is not in the bin..it is included in the following folders

/home/sarah/Fiji.app/bin/cmtk/include/cmtk/Registration

Is this the folder I was looking for with ls /home/sarah/Fiji.app/bin/cmtk/bin/registration ? Do I need to move it somewhere else?

Cheers,
Sarah