help > Totally lost
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Jun 15, 2016  03:06 AM | Ottar Gislason - none
Totally lost
I'm trying to install JIST on an ubuntu machine, but I'm not even quite sure of what JIST is/does.

I've installed it as a plugin for MIPAV, but I was instructed to install it also as a standalone. My problem is I'm not really familiar at all with any of this software and it's unclear to me what's what. On the downloads page I see mostly stuff which is marked as MIPAV bundles, which is what I set up as a plugin. But then there's the JIST 2.0 stuff which I guess is probably the standalone, but it's from 2010.. is that normal? I tried downloading it but when I try to execute the .jar file it says its not an executable and is "not marked as executable" and something about executable bits.

If anyone can point me in the right direction it would be greatly appreciated.

Sorry for my ignorance, I'm just a research assistant newbie with limited linux experience and essentially zero neuro/image experience.
Jun 15, 2016  04:06 AM | Andrew Plassard
RE: Totally lost
Hi Ottar,
What are you looking to do with JIST? That will help us point you in the right direction.

You most likely will need to download this version of JIST, which is the version 3.2 release, and install it into MIPAV following 

JIST typically needs to be installed in MIPAV to run, but what it sounds like you want is the command line interface ( This is also wrapped nicely in PyJIST (

Hope that helps!
Jun 15, 2016  05:06 AM | Ottar Gislason - none
RE: Totally lost
Thanks for the response Andrew,

So there's no sort of standalone client for JIST? I was operating under the impression that I should be able to find some sort of client so no wonder I was confused.

To answer your question as to what I plan on doing, I honestly have no idea. I just started as an research assistant and was instructed to install all sorts of neuroimaging related stuff but my boss isn't in the country for another week so I'm just sort of blundering my way through.

I have already installed the JIST plugin into MIPAV and it appears to work. So my next step would be to install the CLI? Or is that included automatically? Does PyJIST have a GUI or is it just to simplify the CLI commands?
Jun 15, 2016  06:06 AM | Andrew Plassard
RE: Totally lost
If you want a GUI for JIST, there are several options within the MIPAV plugin depending on what you do.

The JIST CLI is also installed when you install the JIST plugin into MIPAV. You will just need to follow the tutorial I sent before to understand how it works. PyJIST is a simplification of the CLI commands to hide things like setting the java class path.