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
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.


On 22 Aug 2017, at 14:39, R. Duke <[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
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
    T: +44 1865 617657
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
Governing Body Fellow, Wolfson College, Oxford.        
Research Fellow, FMRIB Centre