Nate,
I can spot a few issues with the command that you might want to check:
The input to '-t' would normally be a transformation matrix (i.e. a .mat). Also the -S option cannot appear on its own it needs to point to the standard space image you are using (or leave it out if you are happy with the MNI152 one that comes with FSL).
If your TR really 200s?
Michael
On 11 Apr 2014, at 13:33, SUBSCRIBE FSL Anonymous <[log in to unmask]> wrote:
> Michael,
>
> I am currently working with some pasl data and I am getting an error after running oxford_asl (listed below). Here is the command I am using.
>
> oxford_asl -i 001_pasl_diffdata.nii.gz -c M0_brain_merge.nii.gz --tis 1.9 -o perfusion_calib --bolus 0.7 --fixbolus --tr 200 --te 12 --slicedt 0.0625 -s t1_struc_brain.nii.gz --regfrom M0_brain.nii.gz --asl2struc M0_2_t1.mat --pvcorr -t 001_t1_struc_brain.nii.gz --structout -S --report --norm
>
> There also seems to be an issue with the output. The perfusion images in my native_space and struct_space directories do not look correct. They appear to have a high intensity to low intensity gradient running from posterior to anterior. Also, my std_space directory is empty. Do you see any problems with the options I have included?
>
> I am running FSL 5.0.6
>
> Thank you,
>
> Nate
>
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_31i0C2_asl_calib/seg_bias
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/asl_calib: line 568: 17836 Aborted (core dumped) ${FSLDIR}/bin/applywarp --ref=$calib --in=$temp_calib/seg_bias --out=$temp_calib/biasfield --premat=$temp_calib/high2low.mat --super --interp=spline --superlevel=4
> Cannot open volume /tmp/fsl_31i0C2_asl_calib/biasfield for reading!
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_31i0C2_asl_calib/sens
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/asl_calib: line 689: 17846 Aborted (core dumped) fslmaths $temp_calib/calib -div $temp_calib/sens $temp_calib/calib
> Image Exception : #22 :: ERROR: Could not open image --report
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/oxford_asl: line 172: 18234 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2std.mat -ref $std -out $outdir/std_space/$subdir/$parname
> Cannot open volume perfusion_calib/std_space///perfusion for reading!
> Image Exception : #22 :: ERROR: Could not open image --report
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/oxford_asl: line 172: 18307 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2std.mat -ref $std -out $outdir/std_space/$subdir/$parname
> Image Exception : #22 :: ERROR: Could not open image --report
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/oxford_asl: line 172: 18363 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2std.mat -ref $std -out $outdir/std_space/$subdir/$parname
> Cannot open volume perfusion_calib/std_space///perfusion_wm for reading!
> Image Exception : #22 :: ERROR: Could not open image --report
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/oxford_asl: line 172: 18422 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2std.mat -ref $std -out $outdir/std_space/$subdir/$parname
> Cannot open volume perfusion_calib/native_space///deltwm for reading!
> Cannot open volume perfusion_calib/std_space///perfusion for reading!
> Cannot open volume perfusion_calib/std_space///perfusion_wm for reading!
>
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