Dear Michael,

After some digging I came to the same conclusion. I adjusted the number of TIs to the number of repeats I used and that seems to have solved it. I did not have this problem before when I used the same command line I used now. I thought that oxford_asl extrapolates TIs if the amount is not the same as the repeats, but it seems I was mistaken. So the adjustment was just from 

oxford_asl -i %s/nifti/diffdata.nii.gz --tis 0.5,0.75,1,1.25,1.5,1.75,2,2.5,2.75 -o %s/FirstAnalysis --bolus 1.1 --bat 0.7 --t1 1.3 --t1b 1.66 -c %s/M0/M0brain.nii.gz -s $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --cgain 1 --regfrom %s/mask/registration.nii.gz --spatial --report

to

oxford_asl -i %s/nifti/diffdata.nii.gz --tis 0.5,0.75,1,1.25,1.5,1.75,2,2.5,2.75,3 -o %s/FirstAnalysis --bolus 1.1 --bat 0.7 --t1 1.3 --t1b 1.66 -c %s/M0/M0brain.nii.gz -s $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --cgain 1 --regfrom %s/mask/registration.nii.gz --spatial --report

Thank you very much for you time and apologies that I did not figure this out earlier. 

With kind regards,

Daan van den Oever
Master student Technical Medicine

On Wed, Oct 14, 2015 at 4:19 PM, Michael Chappell <[log in to unmask]> wrote:
Daan,

This is odd and sounds like it has something to do with the setting of the TIs inside oxford_asl. What is the command line call you are using? What TIs and number of repeats are there in your data? It looks from the error you had before that your data has 10 volumes?

Michael


On 13 Oct 2015, at 13:33, Daan van den Oever <[log in to unmask]> wrote:

Hi Matthew,

I have modified the file but now I get this error five times:

Welcome to FABBER v2.0
Logfile started: /tmp/fsl_V0k80d_ox_asl/basil/step1/logfile
Start time: Tue Oct 13 14:28:52 2015
FABBER release v2.0 
    Forward Model version:
      $Id: fwdmodel_asl_grase.cc,v 1.22 2013/09/04 15:13:00 chappell Exp $
    Loading mask data from '/tmp/fsl_V0k80d_ox_asl/mask'
    Loading data from '/home/daan/Desktop/PIN43218_t0//nifti/diffdata.nii.gz'
Invalid_option exception caught in fabber:
  

An exception has been thrown
Runtime error:- Data length (10) does not match model's output length (9)!Trace: VariationalBayesInferenceTechnique::DoCalculations; FABBER main(); FABBER main (outer).



Usage: fabber <arguments>
Arguments are mandatory unless they appear in [brackets].
Use -@ argfile to read additional arguments from a text file.

  [--help] : print this usage message
  --output=/path/to/output : put output here (including logfile)
  --method={vb|spatialvb} : use VB (or VB with spatial priors)
  [--max-iterations=NN] : number of iterations of VB to use (default: 10)
  [--data-order={interleave|concatenate|singlefile}] : should time points from multiple data be interleaved (e.g. TE1/TE2) or left in order? (default: interleave)
  --data1=file1, [--data2=file2]. (use --data=file instead if --data-order=singlefile)
  --mask=maskfile : inference will only be performed where mask value > 0
  --model={quipss2|q2tips-dualecho|pcasl-dualecho} : forward model to use. For model parameters use fabber --help --model=<model_of_interest>
  --noise={ar1|white} : Noise model to use
    ar1: two AR(1) models (optional cross-linking between TE1 & TE2)
      [--ar1-cross-terms={dual|same|none}] : two types of cross-linking, or none (default: dual)
    white: white noise model, optionally with different noise variances at some data points
      [--noise-pattern=<phi_index_pattern>] : repeating pattern of noise variances for each data point (e.g. --noise-pattern=12 gives odd and even data points different noise variances)
  [--save-model-fit] and [--save-residuals] : Save model fit/residuals files
  [--print-free-energy] : Calculate & dump F to the logfile after each update
  [--allow-bad-voxels] : Skip to next voxel if a numerical exception occurs (don't stop)
For spatial priors (using --method=spatialvb):
  --param-spatial-priors=<choice_of_prior_forms>: Specify a type of prior to use for each forward model parameter.  One letter per parameter.  S=spatial, N=nonspatial, D=Gaussian-process-based combined prior
  --fwd-initial-prior=<prior_vest_file>: specify the nonspatial prior distributions on the forward model parameters.  The vest file is the covariance matrix supplemented by the prior means; see the documentation for details.  Very important if 'D' prior is used.

Any suggestions?

With kind regards,

Daan



On Tue, Oct 13, 2015 at 2:18 PM, Matthew Webster <[log in to unmask]> wrote:
Hello - this might be a regression from 508, can you modify the first line of /usr/lib/fsl/5.0/oxford_asl to read:

#!/bin/bash

and let me know if it fixes your issue.

Kind Regards
Matthew
> Hello all,
>
> Since having updated fsl in Ubuntu yesterday I have been getting error messages when I try to use oxford_asl. I have not changed any settings or values. The error message reads:
>
> /usr/lib/fsl/5.0/oxford_asl: 1176: /usr/lib/fsl/5.0/oxford_asl: alltis[0]=0.1: not found
> /usr/lib/fsl/5.0/oxford_asl: 1176: /usr/lib/fsl/5.0/oxford_asl: alltis[1]=1.5: not found
> Number of inversion times: 2
> Number of timepoints in data: 10
> Number of repeats in data: 5
> /usr/lib/fsl/5.0/oxford_asl: 1190: /usr/lib/fsl/5.0/oxford_asl: Syntax error: Bad for loop variable
>
> If I use bash before calling oxford_asl it seems to work, but I am wondering if something has changed in the oxford_asl pipeline? I could not find anything on the FSL site. And am I supposed to use bash before the command? Thank you.
>
> With kind regards,
>
> Daan van den Oever


---
Michael Chappell MEng DPhil
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