On 1 Nov 2018, at 15:01, Sean Foxley <[log in to unmask]> wrote:

Hi guys,

I'm helping a colleague with getting oxford_asl working so she can process some ASL data and have encounter an issue. After fabber is called the first time, the command line output runs fine up to a point, where I assume a call to basil is made. At this point the basil syntax is displayed as though I typed basil in the command line with no arguments, and it throws the error

Error! Unrecognised option on command line: --init

After this point, the script essentially fails.

I made an executable copy of the oxford_asl script to try to debug it and found the following:

if [ ! -z $3 ]; then
   # we are being supplied with an intial MVN - pass to BASIL
   initmvn="--init $3"
   Log "Initial MVN for BASIL is: $3"
else
   initmvn=""
fi

If I comment out 'initmvn="--init $3"' in the if statement and instead put in a blank variable (initmvn=""), it gets past this error and oxford_asl seems to run through to completion; however, the second instantiation of fabber says

STEP 2: Spatial VB (2 param: CBF and ^t) - init with STEP 1

I suspect that in the first call that basil needs a finalMVN.nii.gz for the --init flag to function, but that file doesn't exist yet, and is instead an output of the first call that is used in the second call, but this is just a guess. I haven't read the code that closely nor do I know any of these tools that well. Any ideas or help you might heave would be much appreciated.

Cheers,
sean

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