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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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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