Michael & Experts,
After running the command listed below I end up with the error at the bottom of this inquiry. In my native_space directory the gm and wm masks are empty (as expected from the error listed). I feel that I have included all of the appropriate images/options but it appears that asl_calib is having a problem referencing the tissue masks. Have I inadvertently failed to include a specific option or image in my command line? I am running FSL 5.0.6
oxford_asl -i pasl_diffdata.nii.gz -c M0_brain_merge.nii.gz --tis 1.9 -o perfusion_calib --bolus 0.7 --fixbolus --tr 3.4 --te 12 --slicedt 0.0625 -s t1_struct_brain.nii.gz --regfrom M0_brain.nii.gz --asl2struc M0_2_t1_2.mat --report --norm > junk_perfusion_calib.txt
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_kylrxb_asl_calib/seg_bias
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/asl_calib: line 568: 9974 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_kylrxb_asl_calib/biasfield for reading!
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_kylrxb_asl_calib/sens
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/asl_calib: line 689: 9984 Aborted (core dumped) fslmaths $temp_calib/calib -div $temp_calib/sens $temp_calib/calib
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
Thank you,
Nate
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