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​Hi Michael,


I think you are right since I noticed that if I typed "bash" before oxford_asl  the command would work.  I made the switch to my shebang line and it works (at least i think it does, my cluster users will test it out more).   I had no idea that bash had different arrays than sh.


Have a nice day!

Thomas

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Michael Chappell <[log in to unmask]>
Sent: Thursday, March 9, 2017 7:08 AM
To: [log in to unmask]
Subject: Re: [FSL] oxford_asl: alltis[0]=1.4: not found
 
This is a good point, but given the output I suspect this is okay - the image contains a single volume corresponding to a single repeats of the TI.
What could be an issue here is to do with the shell, this particular part of oxford_asl relies on bash style arrays, but it is possible on this system the default shell doesn’t handle arrays. Try changing the first line of oxford_asl from 
#!/bin/sh
to 
#!/bin/bash
and see if that makes any difference.

Michael


On 9 Mar 2017, at 08:27, Pieter Vandemaele <[log in to unmask]> wrote:

Hi Thomas,

I am not an expert and I don't know if this is correct, but maybe it is necessary that the number of 3D images in your input images is the same as the number of TIs taking into account repeats.
Maybe you can check if this is the problem (and preferably let it know in the mailing list ;-) )
Good luck

Pieter

Op 8/03/2017 om 17:24 schreef Thomas Beaudry:
Hi Everyone,

I'm trying to run the following command and run into this error.  Any help would be greatly appreciated!

user@perf-hpc01:~/asl/mMPI/asl_pipleline/P02/D0$ oxford_asl -i pwi1 -o cbf_1 -c m0_mean --bolus 0.7 --t1 2 --t1b 2.2 --tis 1.4 --cmethod voxel --t1t 2 --tr 10.0 --bat 0.7
OXFORD_ASL - running
Creating output directory
Saving results in natve (ASL aquisition) space to cbf_1/native_space
Pre-processing
Creating mask
/util/packages/FSL/5.0.9/bin/oxford_asl: 1176: /util/packages/FSL/5.0.9/bin/oxford_asl: alltis[0]=1.4: not found
Number of inversion times: 1
Number of timepoints in data: 1
Number of repeats in data: 1
/util/packages/FSL/5.0.9/bin/oxford_asl: 1190: /util/packages/FSL/5.0.9/bin/oxford_asl: Syntax error: Bad for loop variable


Thanks!
Thomas

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Pieter Vandemaele, MSc-Ing
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Ghent Institute for Functional and Metabolic Imaging
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---
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.
    http://www.wolfson.ox.ac.uk        
Research Fellow, FMRIB Centre