On 4/23/08, Gregory Lee <[log in to unmask]> wrote:

Michela,

I think the problem is that /bin/sh on Solaris is probably the original Bourne shell, not the GNU bash shell (Bourne-Again Shell) commonly used for /bin/sh in linux distributions. Apparently some of the FSL scripts require extended syntax that is only supported by bash shell.

I had the same errors at one point on Ubuntu linux. On Ubuntu versions since 6.10 /bin/sh links to dash instead of bash by default. I would get the same failures as you mentioned. Changing the /bin/sh link to point to /bin/bash instead of /bin/dash fixed the problem for me.

- Greg

However, I now fixed the problem by changing the shell from:

/bin/sh

to

/bin/bash

in the following scripts:

fsl_sub
bedpostx
bedpostx_postproc.sh
bedpostx_preproc.sh
bedpostx_datacheck
bedpostx_single_slice.sh

After these changes, I re-run the evaluation for all FSL programs and it seemed to work fine. I reported the output below.
Don't know if this makes sense. /bin/sh on solaris was not able to interpret some command in the above files. Here is just one example of what I mean (referring to FSLDIR/bin/bedpostx):

sh couldn't recognize this statement:

if [ ! -e ${subjdir}/bvecs ]; then

but would work with this:

if [ ! -f ${subjdir}/bvecs ]; then

If you have any idea why this happens, it would be very helpful for me!
Thanks,
Michela