[Neurodebian-users] FSL: randomise_parallel not defragmenting......

[Yaroslav Halchenko]

On Tue, 03 Dec 2013, Jonathan Brooks wrote:
> I’m trying to run some randomise_parallel jobs on our cluster (SGE, running on Ubuntu/Debian) and although the SEED images are being generated, they are not being defragmented. If I look in LAc30_logs/LAc30.defragment.e1332 I see a whole load of these errors:

> /rdsfhome/om7253/Documents/Group/RANDOMISE/OUTPUT/LAc30/LAc30.defragment: 1: /rdsfhome/om7253/Documents/Group/RANDOMISE/OUTPUT/LAc30/LAc30.defragment: Bad substitution

> ….
> ….
> lots and lots….

> Any tips on how to over-come this? FYI we’re using the neurodebian FSL repositories (5.0.4 - I think).

there was a recent report which is probably of relevance to you (about bashisms
in fsl's scripts while ubuntu -- I bet that is what you have -- using dash as
bin/sh).  so try just changing your shell to be bash across nodes and see if
helps.

Date: Thu, 31 Oct 2013 13:55:52 +0000
From: "Shpaner, Marina" <Marina.Shpaner at vtmednet.org>
To: "'neurodebian-users at lists.alioth.debian.org'" <neurodebian-users at lists.alioth.debian.org>
Subject: Re: [Neurodebian-users] FSL randomise not finishing the job

   The problem turned out to be on the randomise side. We had to change sh to
   bash, and it worked like a charm. Thank you for your reply, and sorry for
   the trouble.
 

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik