itksnap Command Line tool on Windows?

[David Wikström]

Hi,

I've installed ITK Snap 3.6.0 from the ITK Snap Downloads page on both Windows and Mac OS.

On MacOS, command line works just fine, but I can't seem to find any command line tools on Windows.

Is this an actual limitation of the Windows version, or am I simply doing something wrong?

/Thanks!

[Paul Yushkevich]

The directory containing ITK-SNAP.exe needs to be added to your Windows path. Here is a little article for doing it on different Windows versions:

https://www.java.com/en/download/help/path.xml

In your case, the directory will likely be C:\Program Files\ITK-SNAP 3.6\bin

The current "experimental" build of ITK-SNAP (version 3.8-alpha) will offer to do this for you during the installation process.

Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[David Wikström]

Thanks Paul!

I know how to reference the full path of the exe, so it seems in the end the issue was simply that the options don't seem to be the same on Mac and Windows. I used -h on the Mac just as a simple test to see if command line was working, but is seems use -help on Windows...

Also kind of quirky that you seem to need to use itk-snap on Windows and itksnap on the Mac, but once you know it, it's obviously not a big deal.

[Sarah Blackledge]

Hi,

I have a related issue with itk-snap version 4.0.0. I've installed this version on Windows 10. I can successfully open itk-snap from the command line by typing 'itk-snap' (with the hyphen) as suggested in this thread.

However, I'd like to open a specific itksnap workspace file from the command line. I can open the usage information from the command line by typing 'itksnap-wt' (no hyphen here weirdly enough). See below for an excerpt of the text that pops up in the command prompt:

itksnap_ws : ITK-SNAP Workspace Tool

Usage:

     itksnap_ws [commands]

I/O commands:

    -i <workspace>                               : Read workspace file

...

When I try to run itksnap_ws -i <workspace> from the command line (following the instructions above), I get the following error message:

'itksnap_ws' is not recognized as an internal or external command,
operable program or batch file.

Can anyone help me troubleshoot? Is there some additional exe that I need to download or add to the Windows path?

Many thanks,

Sarah

[Paul Yushkevich]

Hi Sarah 

Thank you for reporting this issue. Note that itksnap-wt is a separate workspace management tool. To launch the main program you need to run itksnap. 

However it sounds like that program is not in your path which may be an issue with the windows build of 4.0.0

Thank you!

Paul

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[Sarah Blackledge]

Hi Paul,

Thanks so much for getting back to me. I managed to figure out the problem. I was typing itksnap_ws [commands] (based on the usage information printed to the command prompt after typing itksnap-wt). 

However, I think the usage info contains a typo, as itksnap_ws doesn't exist. I managed to get it to work by typing itksnap-wt [commands]. I had to do quite a bit of trial and error with the right combination of hyphens/underscores/wt/ws, but managed to work it out in the end!

Best wishes,

Sarah

[Sarah Blackledge]

Scratch that - I thought I had it working last night, but I really just got the absence of an error message.

In case anyone is interested, the following actually works:

itk-snap -w [commands]

Cheers!

Sarah