I presume it runs if you do not add the ‘-c’ option? I think that it is expecting a structural image to generate a CSF mask for calibration - as that is our default approach in the current version. If you want to do it without a CSF mask, i.e. voxelwise calibration, then it might be easier, at the moment, to do that to the perfusion image after oxford_asl has run.
Michael
> On 18 Jun 2016, at 18:43, Ishtiaq Mawla <[log in to unmask]> wrote:
>
> Hi experts, I am receiving the following error while running
> oxford_asl. What's wrong? Thank you for your help!
>
> oxford_asl -i /cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP038_1A/pcASL/preASL/pcASL_pre_mc_bet_diff.nii.gz
> -o /cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP038_1A/pcASL/preASL --tis
> 2.7 --casl -c /cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP038_1A/pcASL/preASL/pcASL_aveCTRL.nii.gz
> OXFORD_ASL - running
> Pre-processing
> Cannot open volume /tmp/fsl_9bJS2Z_ox_asl/calib for reading!
>
> Error: input image /tmp/fsl_9bJS2Z_ox_asl/calib not valid
>
> Creating mask
>
> Error: input image /tmp/fsl_9bJS2Z_ox_asl/calib not valid
>
> Cannot open volume /tmp/fsl_9bJS2Z_ox_asl/calib_bet for reading!
> Calculating M0a - calling ASL_CALIB
> ASL_CALIB
> Tissue reference is: csf
> Cannot open volume /tmp/fsl_9bJS2Z_ox_asl/struc for reading!
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9bJS2Z_ox_asl/struc
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 569: 32313 Aborted
> (core dumped) fast -b -o $temp_calib/seg -p $struc
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9bJS2Z_ox_asl/struc
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 569: 32399 Aborted
> (core dumped) flirt -in $struc -ref
> $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -omat
> $temp_calib/struc2std.mat
> Could not open matrix file /tmp/fsl_9ULbmY_asl_calib/struc2std.mat
> Cannot read input-matrix
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9bJS2Z_ox_asl/struc
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 569: 32410 Aborted
> (core dumped) flirt -in $temp_calib/VentricleMask
> -applyxfm -init $temp_calib/std2struc.mat -ref $struc -out
> $temp_calib/mask
> Cannot open volume /tmp/fsl_9ULbmY_asl_calib/refpve for reading!
> Could not open matrix file /tmp/fsl_9bJS2Z_ox_asl/asl2struct.mat
> Cannot read input-matrix
> Could not open matrix file /tmp/fsl_9ULbmY_asl_calib/high2low.mat
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9ULbmY_asl_calib/refpve
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 569: 32414 Aborted
> (core dumped) applywarp --ref=$calib
> --in=$temp_calib/refpve --out=$temp_calib/refmask
> --premat=$temp_calib/high2low.mat --super --interp=spline
> --superlevel=4
> Could not open matrix file /tmp/fsl_9ULbmY_asl_calib/high2low.mat
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9ULbmY_asl_calib/seg_bias
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 569: 32417 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_9ULbmY_asl_calib/biasfield for reading!
> Cannot open volume /tmp/fsl_9ULbmY_asl_calib/refmask for reading!
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9ULbmY_asl_calib/refmask
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 574: [: : integer
> expression expected
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9ULbmY_asl_calib/sens
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 690: 32425 Aborted
> (core dumped) fslmaths $temp_calib/calib -div
> $temp_calib/sens $temp_calib/calib
> Image Exception : #22 :: ERROR: Could not open image
> /tmp/fsl_9ULbmY_asl_calib/refmask
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/asl_calib: line 690: 32427 Aborted
> (core dumped) fslmaths $temp_calib/calib -mas $mask
> $temp_calib/calib
> M0:151.38000000000000000000
> ASL_calib - DONE.
> Number of inversion times: 1
> Number of timepoints in data: 46
> Number of repeats in data: 46
> 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7
> 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7
> 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7
> Setting up BASIL
> Calling BASIL on data
> Creating output directory: /tmp/fsl_9bJS2Z_ox_asl/basil
> Model for analysis is: buxton
> Using bolus length: 1
> STEP 1: VB (2 param: CBF and ^t)
> ------------------
> Welcome to FABBER v2.0
> Logfile started: /tmp/fsl_9bJS2Z_ox_asl/basil/step1/logfile
> Start time: Sat Jun 18 13:41:14 2016
> FABBER release v2.0
> Forward Model version:
> $Id: fwdmodel_asl_grase.cc,v 1.22 2013/09/04 15:13:00 chappell Exp $
> Loading mask data from '/tmp/fsl_9bJS2Z_ox_asl/mask'
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_9bJS2Z_ox_asl/mask
> NEWMAT exception caught in fabber:
>
>
> An exception has been thrown
> ERROR: Could not open image /tmp/fsl_9bJS2Z_ox_asl/maskTrace:
> read_volumeROI; LoadData; FABBER main(); FABBER main (outer).
>
> Logfile was: /tmp/fsl_9bJS2Z_ox_asl/basil/step1/logfile
> End.
> Cannot open volume /tmp/fsl_9bJS2Z_ox_asl/basil/step1/mean_ftiss for reading!
> Cannot open volume /tmp/fsl_9bJS2Z_ox_asl/basil/step1/mean_delttiss for reading!
> Cannot open volume
> /cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP038_1A/pcASL/preASL/native_space///perfusion
> for reading!
> Output is /cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP038_1A/pcASL/preASL/
> OXFORD_ASL - done.
