Dear Inge,
Your call to oxford_asl looks correct and so should work. The error you are seeing is not a direct error from oxford_asl but from one of the sub components it called (in this case basil itself). I think that the number of repeats in your data is being calculated incorrectly by oxford_asl internally, this would normally be excuse there is a mismatch in the number of volumes in your data and the number of TIs you have specified. As a sanity check can you run fslinfo on your 4D_Dataset.nii.gz and see what it says, please?
Thanks,
Michael
On 2 May 2013, at 12:07, Inge R. Groote <[log in to unmask]> wrote:
> Hi!
>
> I have tried to compute CBF-maps from a set of pCASL multi-TI measurements, adhering to examples in the BASIL tutorial and relentlessly reading the documentation. I´m caught in a desperate state of confusion, and hereby ask the Community for help with some basic operations in order to get forward.
>
> My set has nine TIs, these have been subtracted and neatly packed in a single .nii-file, and should (as I understand it) be ready to give CBF and BAT. Giving the simplest command:
>
> oxford_asl -i 4D_Dataset.nii.gz --tis 0.8,1.0,1.2,1.4,1.6,1.8,2.0,2.2,2.4 -o Output_folder --bolus 1.65 --bat 0.7 --t1 1.3 --t1b 1.66
>
> and simpler variations thereof, crashes, and I am communicated that:
>
> Runtime error:- Option requires a value: --repeats (or omit, equivalent to --repeats=1Trace: InferenceTechnique::Setup; VariationalBayesInferenceTechnique::Setup; FABBER main(); FABBER main (outer).
>
> Trying to trace the "--repeats", I find in the documentation that a "-@-file" should be specified, but nothing in the command points to this "-@". Also, trying to chuck in "--repeats=1" in the command helps nothing.
>
> How can I proceed?? A fresh basket of fruit to whom can give help!
>
> Kind regards;
>
> Inge
>
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