I am trying to set up slicer (https://www.slicer.org/wiki/Main_Page) so I can use the slicer interfaces in nipype. However, I can only get slicer working via the gui and get “command not found” when I attempt to run any of the commands via the terminal to check whether nipype would work. If anyone knows how to set up slicer to work with nipype, please could you let me know how you did this?
Ahoi hoi @brendan.williams,
thank you very much for your post and welcome to neurostars, it’s
great to have you here. I’m truly sorry for the delayed reply.
Did you resolve your issue yet? Could you maybe provide more information and some code snippets so that folks here can better understand and reproduce your problem? I personally never used slicer (neither in its’ GUI form nor through nipype), thus I can’t really be of help here I think. What I know from other interfaces is that it’s important to check the environments you’re using and that the paths to the respective binaries you want to use are set correctly. The install section of the outdated Nipype Beginner’s Guide provides some pointers (unfortunately not
slicer as mentioned here). The only example that uses
slicer I found is this one here.
HTH, cheers Peer