[Neurodebian-users] Ubuntu 10.10, csh or tcsh and FSL 4.1

[Deryk S. Beal, Ph.D.]

Hi Michael

My apologies. I am, obviously, not a programmer. Unfortunately I was working
under the assumption that the trac-all command had to be used within a csh
or tsch environment. As such, I never attempted to run the trac-all command
from bash (or some other non-c alternative). At your suggestion I started
the trac-all command in bash and it appears to be running without error.

Although it may be a moot point, it seems that when running trac-all in
csh/tcsh with the Neurodebain distro of FSL one must alter the routines
called from "flirt" to "flirt.fsl." in order for them to be sourced
correctly. However, as you pointed out there are good reasons not to operate
within csh/tcsh and trac-all appears to be running without error under bash.

Thanks again for your timely support.

Cheers,
Deryk

Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Department of Cognitive and Neural Systems Speech Laboratory
Boston University, 677 Beacon Street, Boston, MA 02215
dsbeal at bu.edu
http://blogs.bu.edu/dsbeal/about/
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On Thu, Jun 9, 2011 at 12:35 PM, Michael Hanke <mih at debian.org> wrote:

> On Thu, Jun 09, 2011 at 12:15:24AM -0400, Deryk S. Beal, Ph.D. wrote:
> > Hi Michael
> >
> > Thank you for the quick reply and the advice on an adequate shell for
> both
> > FS and FSL.
> >
> > The commands I had difficulty with stem from the use of FS5.1.0 and the
> > trac-all - prep command that calls a number of FSL routines. The
> > configuration file and the routines that it calls seem to be written for
> > csh/tcsh.
>
> Even if that command uses csh inside, it should inherit all settings from
> a parent non-csh shell. Are you running the example call you gave in a
> csh session or in some other shell?
>
> FSL also has several commands that rely on csh -- and they work just
> fine when ran from bash/dash/zsh/...
>
> > I have encountered errors, and still do even with fslmachtype.sh and the
> csh
> > apparently working correctly, that imply that my FSL distro is not
> sourced
> > properly. Here is an example of the output from trac-all -prep -c when it
> > faults before even processing one subject (thank you in advance for any
> > advice):
>
> Yes, the csh config shipped with the package is not appropriate (it is
> what comes with stock FSL, untouched). But in general you should not
> need it, as long as you don't insist on running csh as your interactive
> shell.
>
> Let me know,
>
> Michael
>
> --
> Michael Hanke
> http://mih.voxindeserto.de
>
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