controling PuTTy through Matlab

My task is this: I need to open PuTTy on a Windows machine, connect to a Linux box, start a program (FreeSurfer) on that box and run some commands. I tried using the FileExchange's "SSH From Matlab (updated) + SFTP/SCP", but I could not run the FreeSurfer commands once I started it, so I figured I could use tcpip to communicate with PuTTy on the Local machine; however, I don't know how to connect to PuTTy using Matlab on the Windows machine. I believe this is a case for using the tcpip commands, but I'm lost. I think the first step might be:

t = tcpip('localhost',<port for talking with PuTTy>);

but I have no idea what port I should choose.

Any help would be appreciated.

Answer 1

[Jason Ross]

Rather than using PuTTY, you might want to try using plink, which is part of the PuTTY suite and is much more geared to CLI operation:

http://the.earth.li/~sgtatham/putty/0.58/htmldoc/Chapter7.html

Overall, though, your question is a little confusing. As I understand it, PuTTY is a client program that allows connection via various protocols (SSH, rsh, Serial, Telnet, etc) but your must be running something to connect to. I'm guessing that may be the FreeSurfer program? Or are you using rsh or ssh as the protocol?

Also, if possible I would recommend keeping this communication as simple as possible. If you could script the startup of the remote program in some manner and only send over one command, that would be much better than trying to interact. It doesn't need to be anything grandiose, either -- likely a shell script that would take input arguments and then pass them on to the startup command, and return an appropriate exit status would likely be enough.

[Daniel]

Thanks for the input Jason. To clarify my question, I have two machines, the windows one, which does the data processing and higher level functions, and a linux one, which houses the data. Before I can process the data I need to get some information about about which data files correspond to what. Currently this is done by connecting to the linux machine using PuTTy, launching the program Freesurfer (which is a command line program) and running a simple command. This is easy enough for me, but apparently too much work for other people who are using my tools and they want this portion automated so they can open Matlab, click a button and it will talk to the linux box, run the necessary commands over there, and then download the data to the local windows machine. Make sense?

[Jason Ross]

Yep. Makes sense.

In the spirit of "alternate design", have you considered doing this through http? It would handle a lot of the connection setup, teardown, concurrency, etc for you.

[Jason Ross]

Of course, that adds in the additional complexity of the webserver and setting up some form of interface that will query the freesurfer program, then return said data in some format. Which could also run into problems depending on the size of the data set returned.

One door closes, two open, I guess :)