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
> W: 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
> Director of Training, EPSRC-MRC CDT in Biomedical Imaging
> http://www.onbi.ox.ac.uk
> Governing Body Fellow, Wolfson College, Oxford.
> http://www.wolfson.ox.ac.uk
> Research Fellow, FMRIB Centre
> http://www.fmrib.ox.ac.uk
>
>
>
>
>
