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Subject:

Re: suppressing graphics in SPM 2

From:

"Stephen J. Fromm" <[log in to unmask]>

Reply-To:

Stephen J. Fromm

Date:

Fri, 21 Sep 2007 12:57:11 +0100

Content-Type:

text/plain

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text/plain (59 lines)

On Fri, 21 Sep 2007 12:00:49 +0100, <John> <Gelburg> 
<[log in to unmask]> wrote:

>Hi,
>
>I would like suppress the graphics in SPM 2 (all those windows, which are
>opened during processing of fMRI images). I tried to run the matlab in 
mode:
>matlab -nodisplay -nojvm, but I am still getting the windows opened.
>
>Interestingly, when just for test I run the command: spm ('Welcome') I am
>getting "Can't open any graphics windows..." error message. In addition, I
>tried to run the matlab in non graphical console, but then SPM complains,
>that it can't open UI elements.
>
>Is it feasible to run SPM without graphics output? I am running it 
remotely
>via Internet connection and the processing is enormously slow because of 
it.

I can't comment on the feasibility of running SPM w/o graphics mode, 
though my best guess is that it might not be that simple.

On the other hand, there might be other solutions.

When I first tried working from home, I was connecting from a PC to a 
Solaris (Sun) box.  I used a cheap X-windows server, X-Win32.  It worked 
fine, in the sense it did what it was supposed to do.  But things like SPM 
took _forever_.  I think this was even though I was using DSL, though 
maybe I was using dialup.

My recollection is that the amount of data swapped back and forth was very 
high.  Also, at the time I speculated that the issue wasn't just network 
bandwidth, but also _latency_.  I'm not familiar with the internals of X 
windows, but my impression was that it swaps packets back and forth, and 
it does so much of this that even delays that are not that unreasonable 
(e.g., 50 ms) might start to accumulate.

Eventually, at the suggestion of a colleague, I tried VNC.  This speeded 
things up remarkably, because with VNC you're not running a local X server 
(e.g. on your PC), but rather the VNC protocol, which apparently gives you 
a very quick series of graphical snapshots.  It doesn't _look_ like that, 
but the next effect is to dramatically cut down on bandwidth and latency 
issues.

Using VNC might be a solution to your problems, though I don't know enough 
about your set-up to tell.

(Another advantage over an actual X connection is that under VNC the X 
windows you use live on the same box as the one running matlab.  So if 
your network connection disconnects temporarily, you just reconnect VNC 
and matlab is still alive.  With a true X connection, if the network conn 
dies or hiccups, your windows close and your job dies.  Maybe there's a 
way around that, but I didn't find a simple one.)

>
>Thanks a lot in advance.
>John
>========================================================================

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