The critical error here is:
> fabber: inference_spatialvb.cc:1822: void SpatialVariationalBayes::CalcNeighbours(const NEWIMAGE::volume<float>&): Assertion `checkNofN == 1' failed.
When I have seen that before it was associated with problems to do with the mask. It is worth checking that this doesn't have any isolated voxels within it. A first sanity check before doing that is to make sure you are using a well bahved binary mask, just put it through 'fslmaths mask -bin mask' and try again, it is just possible that might help.
Michael
On 18 Jan 2014, at 04:13, SUBSCRIBE FSL Anonymous <[log in to unmask]> wrote:
> Hello,
>
> I am currently trying to run the BASIL tutorial data (along with my own asl data) and I am dealing with an error after running oxford_asl (asl_file appears to run fine). I have included the error below. I am currently running FSL 5.0.6. Any recommendations on how I might resolve this issue?
>
> Cheers,
>
> Nate
>
> 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_DlxU4S_ox_asl/mask'
> Loading data from 'pcasl_diffdata'
> fabber: inference_spatialvb.cc:1822: void SpatialVariationalBayes::CalcNeighbours(const NEWIMAGE::volume<float>&): Assertion `checkNofN == 1' failed.
> /usr/local/fsl/bin/basil: line 100: 1293 Aborted $fabber --data=$infile --mask=$mask --output=$outdir/step$step --model=$model --max-iterations=$nbiter $allinstruct $vbinstruct $extras -@ $options $1
> End.
> Cannot open volume /tmp/fsl_DlxU4S_ox_asl/basil/step2/mean_ftiss for reading!
> Cannot open volume /tmp/fsl_DlxU4S_ox_asl/basil/step2/mean_delttiss for reading!
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_DlxU4S_ox_asl///ftiss
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/oxford_asl: line 172: 1422 Aborted flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out $outdir/struct_space/$subdir/$parname
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_DlxU4S_ox_asl///delttiss
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/oxford_asl: line 172: 1470 Aborted flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out $outdir/struct_space/$subdir/$parname
> Output is perfusion/
> OXFORD_ASL - done.
>
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