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*
M0:874.5800
ASL_calib - DONE.
Best regards,
Athanasia Mowinckel
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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