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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