Monday, October 08, 2007

GAMMA


Good News. Gamma is still alive. There is no formal support, no official web site. There is a team of long-time users still working on the code, to keep GAMMA compatible with the recent versions of the gcc compiler and to finish the Python bindings. Let's hope for the better. Being Open Source is not a warranty of immortality, but it helps. I am not adding the details here, just because it's unofficial. Mainly I wanted to correct my recent article on this topic.

9 Comments:

At 5:41 PM, Blogger Shaolin said...

Can you tell me if there is new version of GAMMA compatible with the recent versions of the gcc compiler?

I happen to notice there is 4.2.0 version on the website, is it the latest version and where can I download?

 
At 6:00 PM, Blogger old swan said...

As far as I know, Karl Young at UCSF is the coordinator of the work cited by the post. I don't know his email address, though. This web page: http://www.radiology.ucsf.edu/dept/veterans_sect.php contains the address of a Doctor with exactly the same name...

 
At 10:34 PM, Anonymous Philip Semanchuk said...

Hi there,
GAMMA 4.2.0 is alive and well and is available here:
http://scion.duhs.duke.edu/vespa/gamma

I'm one of the developers on the Vespa project which (to quote our Wiki) "is a free software suite composed of three magnetic resonance spectroscopy (MRS) applications... for MR spectral simulation, MR RF pulse design, and spectral processing and analysis of MR data."

Vespa's main page is here:
http://scion.duhs.duke.edu/vespa/project

 
At 8:45 AM, Blogger old swan said...

Dear Philip, one hour ago I typed "svn co http://scion.duhs.duke.edu/guest_svn/gamma/trunk gamma" and nothing has been downloaded yet. Strange way of making things available....

 
At 8:59 PM, Anonymous Philip Semanchuk said...

Hi old swan, all I can recommend is that you try again. It works just fine for me here. My colleague in California occasionally sees SVN checkouts from our server hang on large files, so maybe that's the problem. I see it very rarely here, but I'm just a few miles away from the server so I probably see better behavior than most.

 
At 9:35 PM, Blogger old swan said...

I have downloaded it. Typed "make all" and "make install" without problems. problems started with "make test". I received the error "ImportError: No module named numpy". I have tried to install numpy but the installer says it's impossible because I haven't Python 2.6. Actually I have Python 2.7.1.
No wonder that Linux is such a flop.

 
At 10:21 PM, Anonymous Philip Semanchuk said...

old swan, glad the download worked out.

Did you try installing numpy from your Linux distro's package manager? That's unlikely to get confused about which Python you have installed.

If you're interested in the types of things that GAMMA can do, you should check out the Simulation application that's part of Vespa which allows you to run pulse sequences through GAMMA and visualize the results.

We also have a mailing list for Vespa here:
http://tech.groups.yahoo.com/group/vespa-mrs/

 
At 10:29 PM, Blogger old swan said...

I have a Mac. My main interest is to find something working properly on a Mac. Then I can start playing in my own way, that is to interface this working thing (being it Vespa or Gamma) with the software I use on the Mac (mainly iNMR). The final stage consists into making the fruits of my efforts public. Do you think that Vespa can already substitute Gamma on a Mac? In this case, I will forget about Gamma and install Vespa instead.

 
At 10:59 PM, Anonymous Philip Semanchuk said...

I recommend that you have a look at Vespa. I'm the software lead on the Vespa project and I do all of my development on a Mac so I guarantee that it works under OS X. (Just for the record, we officially support and test Windows and Linux, too.)

However, I'm a software guy, not an NMR guy, so I can't advise you on whether or not Simulation can do what you need it to do. You can read the
Simulation user manual to get an idea. I should also note that Vespa is still in active development so our ears are open to feature requests.

If you have specific questions you can ask on the Vespa mailing list, or you can email me directly and I'll put you in touch with someone who can answer them. My email address is my first name @ my last name.com (also easy to find by Googling my name).

 

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