Hi Anthony,
There is a numerical instability occurring for a couple of voxels in your images, which is not unusual. What should happen is that the voxels be ignored - and indeed the logfile indicates that this is happening earlier in the process.
However the version of Fabber that you have contains a bug where the 'ignore voxel' logic does not occur during the final evaluation of the model where the final MVN and the model fit are output. This bug has been fixed in a more recent version of our ASL analysis tools.
I think the best thing for you to do would be do download and use the latest version of oxford_asl from:
This includes a recent version of the fabber_asl executable which should avoid this error.
All the best,Flora Kennedy McConnell
------------------------------Postdoctoral Research Associate
Department of Engineering ScienceUniversity of OxfordOld Road Campus Research BuildingOxford, UKOX3 7DQ
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Anthony Alexander <[log in to unmask]>
Sent: 14 July 2018 00:07:02Hello Flora and Paul,
I believe we are having a similar issue with step 2 of FABBER, however ours is occurring only at the partial volume correction stage. If this is a different issue I can start a new thread.
We have attempted running through about 5 sets of data and we have the same issue with each one.
Here is the information I have and I would be willing to share our data if you can tell me how.
fsl_ wb1DNR _ox_asl/basil/step1
finalMVN.nii.gz logfile noise_means.nii.gz std_delttiss.nii.gz zstat_delttiss.nii.gz
freeEnergy.nii.gz mean_delttiss.nii.gz noise_stdevs.nii.gz std_ftiss.nii.gz zstat_ftiss.nii.gz
info.txt mean_ftiss.nii.gz paramnames.txt uname.txt
fsl_ wb1DNR _ox_asl/basil/step2
finalMVN.nii.gz mean_delttiss.nii.gz paramnames.txt var_delttiss.nii.gz
freeEnergy.nii.gz mean_ftiss.nii.gz std_delttiss.nii.gz var_ftiss.nii.gz
info.txt noise_means.nii.gz std_ftiss.nii.gz zstat_delttiss.nii.gz
logfile noise_stdevs.nii.gz uname.txt zstat_ftiss.nii.gz
fsl_ wb1DNR _ox_asl/pvcorr/basil/step1
finalMVN.nii.gz mean_ftiss.nii.gz paramnames.txt std_pvwm.nii.gz zstat_pvgm.nii.gz
freeEnergy.nii.gz mean_fwm.nii.gz std_delttiss.nii.gz uname.txt zstat_pvwm.nii.gz
info.txt mean_pvgm.nii.gz std_deltwm.nii.gz zstat_delttiss.nii.gz
logfile mean_pvwm.nii.gz std_ftiss.nii.gz zstat_deltwm.nii.gz
mean_delttiss.nii.gz noise_means.nii.gz std_fwm.nii.gz zstat_ftiss.nii.gz
mean_deltwm.nii.gz noise_stdevs.nii.gz std_pvgm.nii.gz zstat_fwm.nii.gz
fsl_ wb1DNR _ox_asl/pvcorr/basil/step2
info.txt logfile paramnames.txt uname.txt
STEP 2: Spatial VB Tissue PVE - init with STEP 1
----------------------
Welcome to FABBER v3.9.2-78-g7e4027c
----------------------
Last commit: Thu Jan 25 13:00:17 2018
Logfile started: /tmp/fsl_wb1DNR_ox_asl/pvcorr/basil/step2/logfile 1%35371370231.389931 47029505458.779755 1.300000 1.600000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 10.014421 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 10.014421 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 76011042523822017122425372672.000000 96576635593542070815122522112. 000000
0.000000 0.000000 0.000000 0.000000 96576635593542070815122522112.000000 122706467808867387843872292864 .000000
11893025264.716621 103846276214.940628 1.300000 1.600000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 10.014421 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 10.014421 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 8844443584466570525867507712.000000 73798232007530254509063274496. 000000
0.000000 0.000000 0.000000 0.000000 73798232007530254509063274496.000000 615774072775176728573502291968 .000000
35371370231.389931 47029505458.779755 1.300000 1.600000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 10.014421 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 10.014421 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 76011042523822017122425372672.000000 96576635593542070815122522112. 000000
0.000000 0.000000 0.000000 0.000000 96576635593542070815122522112.000000 122706467808867387843872292864 .000000
NEWMAT exception caught in fabber:
An exception has been thrown
Runtime error:- detected by Newmat: matrix is singular
MatrixType = Crout # Rows = 6; # Cols = 6
Trace: Crout(lubksb); GeneralSolvI; InvertedMatrix::Evaluate.
Final logfile: /tmp/fsl_wb1DNR_ox_asl/pvcorr/basil/step2/logfile
End.
Cannot open volume /tmp/fsl_wb1DNR_ox_asl/pvcorr/basil/step2/mean_ftiss for reading!
Cannot open volume /tmp/fsl_wb1DNR_ox_asl/pvcorr/basil/step2/mean_delttiss for reading!
Cannot open volume /tmp/fsl_wb1DNR_ox_asl/pvcorr/basil/step2/mean_fwm for reading!
Cannot open volume /tmp/fsl_wb1DNR_ox_asl/pvcorr/basil/step2/mean_deltwm for reading!
Thank you for any help you can provide,
Anthony
On Thu, Jul 12, 2018 at 4:52 AM, Flora Kennedy McConnell <[log in to unmask]ox.ac.uk> wrote:
Hi Paul,
Thanks for this. We can see where the error is arising - for at least one voxel the number of neighbouring voxels available for consideration in the spatial VB step is zero even though that voxel should be considered as one of its own neighbours.
We're really not sure what about your data could cause this. Would you be willing to share one of the datasets with us so we can have a look at it?
All the best,
Flora
Flora Kennedy McConnell------------------------------Postdoctoral Research Associate
Department of Engineering ScienceUniversity of OxfordOld Road Campus Research BuildingOxford, UKOX3 7DQ
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Paul Mullins <[log in to unmask]>
Sent: 12 July 2018 09:27:40
To: [log in to unmask]
Subject: Re: [FSL] Oxford_ASL - fabber errors.Hi Flora,
we always use a Mac. Have run the analysis successfully on several different macs with different data sets (all produced in the same fashion though, and all from the same study). Ran the command again with debug on as you requested.
The files in Step 1 are :
finalMVN.nii.gz info.txt mean_delttiss.nii.gz paramnames.txt zstat_delttiss.nii.gz
freeEnergy.nii.gz logfile mean_ftiss.nii.gz uname.txt zstat_ftiss.nii.gz
and step 2:
info.txt logfile uname.txt
Hope this helps figure it out.
Paul.
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