Hi Zanariah,

I haven't seen this particular error before, can you let me know which version of oxford_asl you are using? You can find this out by typing: oxford_asl --version into a terminal.

One thing that I notice from your oxford_asl command is that you are providing --pvgm and --pvwm as the pve images from an fsl_anat directory. The inputs for pvgm and pvwm both need to be registered into the native space of your ASL images if you are providing them in this way.

Thanks,

Flora Kennedy McConnell

------------------------------

Postdoctoral Research Associate

Institute of Biomedical Engineering

Department of Engineering Science

University of Oxford

Old Road Campus Research Building

Oxford, UK

OX3 7DQ

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Zanariah Mohd <[log in to unmask]>
Sent: 15 April 2019 15:35:40
To: [log in to unmask]
Subject: [FSL] error: subview::diag(): requested diagonal out of bounds

Hi,

I am running the command: oxford_asl -i Whisper4/PASL.nii -o Whisper4_test -s Whisper4/T1.nii --spatial --tis=1800 --bat=0.7 --t1=1.3 --t1b=1.65 --wp --pvgm fsl_anat_whisper4_test.anat/T1_fast_pve_1.nii --pvwm fsl_anat_whisper4_test.anat/T1_fast_pve_2.nii --vars --report --norm -c Whisper4/M0.nii --tr=3000 --cmethod single --fixbolus --asl2struc

and there is error message:

error: copy into submatrix: incompatible matrix dimensions: 10x1 and 13x1

STL exception caught in fabber:
copy into submatrix: incompatible matrix dimensions: 10x1 and 13x1
Logfile was: /tmp/fsl_YCR8My_ox_asl/basil/step1/logfile
Could not find a supported file with prefix "/tmp/fsl_YCR8My_ox_asl/basil/step1/finalMVN"
Spatial prior specification: MN
STEP 2: Spatial VB (2 param: CBF and ^t) - init with STEP 1
Could not find a supported file with prefix "/tmp/fsl_YCR8My_ox_asl/basil/step1/finalMVN"
------------------
Welcome to FABBER v2.0
Logfile started: /tmp/fsl_YCR8My_ox_asl/basil/step2/logfile
Start time: Mon Apr 15 15:18:04 2019
FABBER release v2.0
    Forward Model version:
      $Id: fwdmodel_asl_grase.cc,v 1.22 2013/09/04 15:13:00 chappell Exp $
Expanded, --param-spatial-priors=MN
    Loading mask data from '/tmp/fsl_YCR8My_ox_asl/mask'
    Loading data from 'Whisper4/PASL.nii'
WARNING ONCE: Not saving finalSpatialPriors.nii.gz -- too huge!!
Reading MVNs from /tmp/fsl_YCR8My_ox_asl/basil/temp
Image Exception : #63 :: No image files match: /tmp/fsl_YCR8My_ox_asl/basil/temp
Image Exception : #22 :: Failed to read volume /tmp/fsl_YCR8My_ox_asl/basil/temp
Error : No image files match: /tmp/fsl_YCR8My_ox_asl/basil/temp

Summary of warnings (1 distinct warnings)
Issued once: Not saving finalSpatialPriors.nii.gz -- too huge!!
STL exception caught in fabber:
Failed to read volume /tmp/fsl_YCR8My_ox_asl/basil/temp
Error : No image files match: /tmp/fsl_YCR8My_ox_asl/basil/temp
Logfile was: /tmp/fsl_YCR8My_ox_asl/basil/step2/logfile
Could not find a supported file with prefix "/tmp/fsl_YCR8My_ox_asl/basil/step2/finalMVN"
End.
Image Exception : #63 :: No image files match: /tmp/fsl_YCR8My_ox_asl/basil/step2/mean_ftiss
terminate called after throwing an instance of 'armawrap::AWException'
what(): No image files match: /tmp/fsl_YCR8My_ox_asl/basil/step2/mean_ftiss
/usr/local/fsl/bin/oxford_asl: line 437: 39883 Aborted                 (core dumped) fslmaths ${finalstep}/mean_ftiss -thr 0 $2/ftiss
Image Exception : #63 :: No image files match: /tmp/fsl_YCR8My_ox_asl/basil/step2/mean_delttiss
terminate called after throwing an instance of 'armawrap::AWException'
what(): No image files match: /tmp/fsl_YCR8My_ox_asl/basil/step2/mean_delttiss
/usr/local/fsl/bin/oxford_asl: line 437: 39886 Aborted                 (core dumped) fslmaths ${finalstep}/mean_delttiss -thr 0 $2/delttiss
Fabber variance calculator
Working in /tmp/fsl_YCR8My_ox_asl/basil/step2
cat: /tmp/fsl_YCR8My_ox_asl/basil/step2/paramnames.txt: No such file or directory
Done.

Does anyone know what should i do?

Thanks,

########################################################################

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1