Dear Brendan,
Thanks for the feedback here.
An easy fix for this is for the imtest script to only worry about
links when it has a full filename, with extension. I'm attaching a
version which does this, and should fix your problem.
All the best,
Mark
On 30 Dec 2011, at 00:55, Brendan Moloney wrote:
> I have found that several FSL commands assume that the base name (the filename without the extension) for input files is unique. For example the command 'bet' will test the input image by doing:
>
> IN=`${FSLDIR}/bin/remove_ext $1`
> OUT=`${FSLDIR}/bin/remove_ext $2`
> shift 2
> if [ `${FSLDIR}/bin/imtest $IN` = 0 ] ; then
> echo ""
> echo "Error: input image $IN not valid"
> echo ""
> exit 1
> fi
>
> This only seems to be an issue when there is a symbolic link with the same base name, as imtest will follow the link before appending the extension and testing if the file exists. I was able to fix this by leaving the extension on the input file (i.e. just setting 'IN=$1'). In the case of bet with the '-S' option I had to do the same thing in the command 'standard_space_roi'. Presumably there are other commands that do the same thing.
>
> Thanks,
> Brendan Moloney
>
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