It looks like something has gone wrong in the creation of the mask. You might try creating your own brain mask from the ASL data (even a crude one to start with) and see if it will then run.
Michael
On 24 Feb 2015, at 23:24, Ishtiaq Mawla <[log in to unmask]> wrote:
> Hi experts, I am receiving the following error message when running BASIL through Asl_gui. I am using pcASL data. Please advise as to what can be done. Thanks!
>
> ------------------
> Welcome to FABBER v2.0
> Logfile started: /tmp/fsl_izco1V_ox_asl/basil/step1/logfile
> Start time: Tue Feb 24 17:24:38 2015
> 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_izco1V_ox_asl/mask'
> Loading data from '/autofs/cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP039_1A/pcASL/preASL/Analysis/native_space/diffData'
>
> *** NEWMAT error while thresholding time-series... Most likely a dimension mismatch. ***
> Mask:
>
> This is fatal... rethrowing exception.
> NEWMAT exception caught in fabber:
>
>
> An exception has been thrown
> Mask of different size used in matrix()Trace: LoadData; FABBER main(); FABBER main (outer).
>
> Logfile was: /tmp/fsl_izco1V_ox_asl/basil/step1/logfile
> End.
> Output is /autofs/cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP039_1A/pcASL/preASL/Analysis/
> OXFORD_ASL - done.
> Image Exception : #3 :: Mask of different size used in matrix()
> Cannot open volume /tmp/fsl_izco1V_ox_asl/basil/step1/mean_ftiss for reading!
> Cannot open volume /tmp/fsl_izco1V_ox_asl/basil/step1/mean_delttiss for reading!
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_izco1V_ox_asl///ftiss
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/oxford_asl: line 173: 20632 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out $outdir/struct_space/$subdir/$parname
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_izco1V_ox_asl///delttiss
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/oxford_asl: line 173: 20681 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out $outdir/struct_space/$subdir/$parname
> OXFORD_ASL - running
> Saving results in structural space to /autofs/cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP039_1A/pcASL/preASL/Analysis/struct_space
> Pre-processing
> Performing registration
> ASL_REG
> Input file is: /autofs/cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP039_1A/pcASL/preASL/Analysis/asldata_mc_even_brain
> Running FLIRT
> Tidying up
> ASL_REG - Done.
> Number of inversion times: 1
> Number of timepoints in data: 46
> Number of repeats in data: 46
> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> Setting up BASIL
> Calling BASIL on data
> Creating output directory: /tmp/fsl_izco1V_ox_asl/basil
> Model for analysis is: buxton
> Using bolus length: 1.4
> STEP 1: VB (2 param: CBF and ^t)
> ------------------
> Welcome to FABBER v2.0
> Logfile started: /tmp/fsl_izco1V_ox_asl/basil/step1/logfile
> Start time: Tue Feb 24 17:24:38 2015
> 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_izco1V_ox_asl/mask'
> Loading data from '/autofs/cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP039_1A/pcASL/preASL/Analysis/native_space/diffData'
>
> *** NEWMAT error while thresholding time-series... Most likely a dimension mismatch. ***
> Mask:
>
> This is fatal... rethrowing exception.
> NEWMAT exception caught in fabber:
>
>
> An exception has been thrown
> Mask of different size used in matrix()Trace: LoadData; FABBER main(); FABBER main (outer).
>
> Logfile was: /tmp/fsl_izco1V_ox_asl/basil/step1/logfile
> End.
> Output is /autofs/cluster/vitaly/jieun/PPG/data/ACUPPG1_LBP039_1A/pcASL/preASL/Analysis/
> OXFORD_ASL - done.
> Image Exception : #3 :: Mask of different size used in matrix()
> Cannot open volume /tmp/fsl_izco1V_ox_asl/basil/step1/mean_ftiss for reading!
> Cannot open volume /tmp/fsl_izco1V_ox_asl/basil/step1/mean_delttiss for reading!
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_izco1V_ox_asl///ftiss
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/oxford_asl: line 173: 20632 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out $outdir/struct_space/$subdir/$parname
> Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_izco1V_ox_asl///delttiss
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /usr/pubsw/packages/fsl/current/bin/oxford_asl: line 173: 20681 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2struct.mat -ref $struc -out $outdir/struct_space/$subdir/$parname
> while executing
> "fsl:exec "$aslCommand""
> (procedure "aslLaunch" line 104)
> invoked from within
> "aslLaunch"
> invoked from within
> ".rename.execute invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .rename.execute"
> (command bound to event)
