Dear list,
I just upgraded my FSL package to the latest version (6.0.1) and ran oxford_asl on a multi-delay ASL data set I had previously analysed using FSL 5.10. Using the previous version, CBF, CBV and calibrated versions of the same, where generated. When using version 6.0.1 - oxford_ASL failed at the FABBER step - producing the error messages attached below.
This would seem to be an error within the program, and not the data, as it ran fine on the old version, but maybe there i something new I need to add to the oxford_asl command line in the new version. Any advice on what to do to "fix" this issue appreciated.
Command used:
oxford_asl -i diffdata.nii.gz -o CBF --tis 0.6,1.12,1.64,2.16,2.68,3.2 --bolus 0.6 -c PDbrain.nii.gz -s brain.nii.gz --regfrom Cont.nii.gz --spatial
Error message starts at FABBER:
STEP 1: VB - Tissue
----------------------
Welcome to FABBER v4.0.1-dirty
----------------------
Last commit: Tue Jan 15 10:39:39 2019
Logfile started: /tmp/fsl_T78VnF_ox_asl/basil/step1/logfile
100%
Image Exception : #77 :: Cannot use setmatrix() with masks with more than 3 dimensions
Exception caught in fabber:
Cannot use setmatrix() with masks with more than 3 dimensions
Final logfile: /tmp/fsl_T78VnF_ox_asl/basil/step1/logfile
Could not find a supported file with prefix "/tmp/fsl_T78VnF_ox_asl/basil/step1/finalMVN"
STEP 2: VB - Tissue Arterial - init with STEP 1
----------------------
Welcome to FABBER v4.0.1-dirty
----------------------
Last commit: Tue Jan 15 10:39:39 2019
Logfile started: /tmp/fsl_T78VnF_ox_asl/basil/step2/logfile
100%
Image Exception : #77 :: Cannot use setmatrix() with masks with more than 3 dimensions
Exception caught in fabber:
Cannot use setmatrix() with masks with more than 3 dimensions
Final logfile: /tmp/fsl_T78VnF_ox_asl/basil/step2/logfile
Could not find a supported file with prefix "/tmp/fsl_T78VnF_ox_asl/basil/step2/finalMVN"
STEP 3: VB - Tissue Arterial Bolus duration - init with STEP 2
----------------------
Welcome to FABBER v4.0.1-dirty
----------------------
Last commit: Tue Jan 15 10:39:39 2019
Logfile started: /tmp/fsl_T78VnF_ox_asl/basil/step3/logfile
0%
erfc underflow error
erfc underflow error
erfc underflow error
erfc underflow error
... (repeats for many iterations)
erfc underflow error
100%
Image Exception : #77 :: Cannot use setmatrix() with masks with more than 3 dimensions
Exception caught in fabber:
Cannot use setmatrix() with masks with more than 3 dimensions
Final logfile: /tmp/fsl_T78VnF_ox_asl/basil/step3/logfile
Could not find a supported file with prefix "/tmp/fsl_T78VnF_ox_asl/basil/step3/finalMVN"
STEP 4: Spatial VB Tissue Arterial Bolus duration - init with STEP 3
----------------------
Welcome to FABBER v4.0.1-dirty
----------------------
Last commit: Tue Jan 15 10:39:39 2019
Logfile started: /tmp/fsl_T78VnF_ox_asl/basil/step4/logfile
0%Exception caught in fabber:
Internal error in Fabber: Coordinate matrix must be in correct order to use adjacency-based priors.
Final logfile: /tmp/fsl_T78VnF_ox_asl/basil/step4/logfile
Could not find a supported file with prefix "/tmp/fsl_T78VnF_ox_asl/basil/step4/finalMVN"
End.
Image Exception : #63 :: No image files match: /tmp/fsl_T78VnF_ox_asl/basil/step4/mean_ftiss
...
Basically from here on, more error messages about TEMP files not existing etc appear. I assume the error happens earlier, and is then propagated through.
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|