Hi,
Also, can you confirm that a file named t1_blood exists in your current directory? It may just be as simple as a missing file error.
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 22 Aug 2017, at 16:42, Michael Chappell <[log in to unmask]> wrote:
>
> By the looks of it the `cat t1_blood` is not doing what you intend - it seems to be passing the string “cat t1_blood” into oxford_asl rather than reading in the value from the file. I am not quite sure what aspect of the shell that is causing this, but presumably if you manually put the relevant number on the command line it will run correctly - which might at least sanity check whether my diagnosis is correct.
>
> Michael
>
>
>> On 22 Aug 2017, at 14:39, R. Duke <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> Hello Experts (Michael),
>>
>> I receive the following error when I run oxford_asl (oxford_asl -i ASL_10TI_diff_mcf.nii.gz -o Oxford_ASL --tis 0.25,0.5,0.75,1,1.25,1.5,1.75,2,2.25,2.5 --t1b `cat t1_blood` --spatial -m M0_mean_brain_mask.nii.gz)
>>
>> Any idea on how to resolve this error?
>>
>> cat: t1_blood: No such file or directory
>> OXFORD_ASL - running
>> Creating output directory
>> Saving results in natve (ASL aquisition) space to Oxford_ASL/native_space
>> Pre-processing
>> Number of inversion times: 10
>> Number of timepoints in data: 10
>> Number of repeats in data: 1
>> 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.25 2.5
>> Setting up BASIL
>> Calling BASIL on data
>> Creating output directory: /tmp/fsl_CNHiDq_ox_asl/basil
>> Model for analysis is: buxton
>> Using bolus length: 1
>> STEP 1: VB (2 param: CBF and ^t)
>> ------------------
>> Welcome to FABBER v2.0
>> Logfile started: /tmp/fsl_CNHiDq_ox_asl/basil/step1/logfile
>> Start time: Tue Aug 22 09:20:35 2017
>> FABBER release v2.0
>> Invalid_option exception caught in fabber:
>>
>>
>> An exception has been thrown
>> Runtime error:- convertTo failed... couldn't convert string '--spatial' into a value.
>> Trace: InferenceTechnique::Setup; VariationalBayesInferenceTechnique::Setup; FABBER main(); FABBER main (outer).\
>>
>> Thank you
>
> ---
> Michael Chappell MEng DPhil
> W: http://www.ibme.ox.ac.uk/qubic <http://www.ibme.ox.ac.uk/qubic>
> T: +44 1865 617657
> Associate Professor, Institute of Biomedical Engineering, University of Oxford.
> http://www.ibme.ox.ac.uk <http://www.ibme.ox.ac.uk/>
> Director of Training, EPSRC-MRC CDT in Biomedical Imaging
> http://www.onbicdt.ox.ac.uk <http://www.onbicdt.ox.ac.uk/>
> Governing Body Fellow, Wolfson College, Oxford.
> http://www.wolfson.ox.ac.uk <http://www.wolfson.ox.ac.uk/>
> Research Fellow, FMRIB Centre
> http://www.fmrib.ox.ac.uk <http://www.fmrib.ox.ac.uk/>
>
>
>
>
>
