Dear Christian,
You seem to be using an old version of FIRST (and thus FSL).
The current version does not use thresholds (e.g. 3) in general
for the boundary correction (although it is still an option, but
not recommended). It is really very different in usage and in
performance.
I suggest you update to the latest version and follow the
instructions in the documentation:
http://www.fmrib.ox.ac.uk/fsl/first/index.html
All the best,
Mark
On 10 Nov 2009, at 09:47, Christian Fiebach wrote:
> Dear FSL experts,
>
> first time users of FIRST (and of FSL); I hope our problem is not
> too obvious,
> but we do not find the solution at the moment.
>
> We are getting the following error:
> fiebach@christian:~/test$ run_first_all structural 3 testout
> /usr/share/fsl/bin/first_flirt structural structural_to_std
> /usr/share/fsl/bin/run_first_all: 168: Bad substitution
> f
>
> -rw-r--r-- 1 fiebach fiebach 0 2009-11-10 10:11
> first_flirt.e6827
> -rw-r--r-- 1 fiebach fiebach 0 2009-11-10 10:12
> first_flirt.e6957
> -rw-r--r-- 1 fiebach fiebach 23 2009-11-10 10:11
> first_flirt.o6827
> -rw-r--r-- 1 fiebach fiebach 53 2009-11-10 10:14
> first_flirt.o6957
> -rw-r--r-- 1 fiebach fiebach 13404884 2009-11-10 09:16
> structural.nii.gz
> -rw-r--r-- 1 fiebach fiebach 144 2009-11-10 10:15
> structural_to_std.mat
> -rw-r--r-- 1 fiebach fiebach 12295241 2009-11-10 10:16
> structural_to_std.nii.gz
>
> I am puzzled by the fact that it appears to me to be the case that
> the process starts during first_flirt (stage2, at least this was the
> last
> output I saw), but line 168 of run_first_all script is obviously quite
> a bit away from the call to first_flirt.
>
> calling first_flirt directly works without error, also when calling
> it using
> fsl_sub as in the run_first_all script.
>
> The other thing I noticed is that our data/first directory contains
> only
> a folder for 336-models, not for 317-models, even though these
> seem to be called from run_first_all.
>
> Any suggestions greatly appreciated! Thanks in advance,
>
> Christian
>
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