Hi.
I'm trying to run an ASL analysis on my data. I have pcASL control-tag data that for the most part are getting run through the analysis without problems. However, there seems to be some difficulties with the calibration.
I'm running the command as root in csh:
oxford_asl -i $INPUT/analysis/diffdata -o $INPUT/analysis/KMI_data --tis 3.6 --bolus 1.8 --bat 1.8 --casl \ --t1b 1.6 --alpha 0.98 --artoff --fixbolus \ --infert1 -s $ANATFOLDER/anat_roi_brain --report \ --regfrom $INPUT/PCASLmean_brain --spatial \ -c $INPUT/M0.nii.gz --tr 12
the error is such:
Number of voxels is:81920 Number of repeats in data is:70 Outputting ASL data mean at each TI Done. OXFORD_ASL - running Creating output directory Saving results in natve (ASL aquisition) space to ASL/analysis/KMI_data/native_space Saving results in structural space to ASL/analysis/KMI_data/struct_space Pre-processing Creating mask Performing registration ASL_REG Input file is: /ASL/PCASLmean_brain Running FLIRT Tidying up ASL_REG - Done. Segmenting the structural image Calculating M0a - calling ASL_CALIB ASL_CALIB Tissue reference is: csf *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/seg_bias* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 568: 58142 Abort trap: 6 ${FSLDIR}/bin/applywarp --ref=$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_SsEGkZ_asl_calib/biasfield for reading!* *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/sens* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 689: 58150 Abort trap: 6 fslmaths $temp_calib/calib -div $temp_calib/sens $temp_calib/calib* M0:874.58000000000000000000 ASL_calib - DONE.
Best regards, Athanasia Mowinckel
That is an FSL program, so you probably don't want advice from the FreeSurfer list! doug
On 05/20/2014 05:29 AM, Athanasia Monika Mowinckel wrote:
Hi.
I'm trying to run an ASL analysis on my data. I have pcASL control-tag data that for the most part are getting run through the analysis without problems. However, there seems to be some difficulties with the calibration.
I'm running the command as root in csh:
oxford_asl -i $INPUT/analysis/diffdata -o$INPUT/analysis/KMI_data --tis 3.6 --bolus 1.8 --bat 1.8 --casl \ --t1b 1.6 --alpha 0.98 --artoff --fixbolus \ --infert1 -s $ANATFOLDER/anat_roi_brain --report \ --regfrom $INPUT/PCASLmean_brain --spatial \ -c $INPUT/M0.nii.gz --tr 12
the error is such:
Number of voxels is:81920 Number of repeats in data is:70 Outputting ASL data mean at each TI Done. OXFORD_ASL - running Creating output directory Saving results in natve (ASL aquisition) space to ASL/analysis/KMI_data/native_space Saving results in structural space to ASL/analysis/KMI_data/struct_space Pre-processing Creating mask Performing registration ASL_REG Input file is: /ASL/PCASLmean_brain Running FLIRT Tidying up ASL_REG - Done. Segmenting the structural image Calculating M0a - calling ASL_CALIB ASL_CALIB Tissue reference is: csf *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/seg_bias* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 568: 58142 Abort trap: 6 ${FSLDIR}/bin/applywarp --ref=$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_SsEGkZ_asl_calib/biasfield for reading!* *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/sens* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 689: 58150 Abort trap: 6 fslmaths $temp_calib/calib -div $temp_calib/sens $temp_calib/calib* M0:874.58000000000000000000 ASL_calib - DONE.
Best regards, Athanasia Mowinckel
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Athanasia Monika Mowinckel -
Douglas N Greve