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Hi Anthony, Sorry to hear that this didn't solve it. I've had a look at the code in comparison to your logfile and there are a few other potential places where this error could be escaping. However it might be easiest to track down if we can reproduce the error locally using your data - are you able to share the data files you're using which produce the error? Many thanks, Martin ________________________________ From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Anthony Alexander <[log in to unmask]> Sent: 01 August 2018 22:52:55 To: [log in to unmask] Subject: Re: [FSL] Oxford_ASL - fabber errors. Hi Flora and Martin, Sorry for the delay. Unfortunately this newer version of Fabber (--version says Fabber v3.9.2-85-g2205738 : Mon Jul 9 14:19:32 2018) did not change anything. We are still getting the error in the exact same spot in the pipeline. I have attached the step 2 log file. Please let me know if you have any other ideas that I can try. Thank you On Wed, Jul 25, 2018 at 5:59 AM, Flora Kennedy McConnell <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Anthony, Thanks, that is all we need. Please see the email below from our software guru Martin. Do let us know how you get on. Flora Kennedy McConnell ------------------------------ Postdoctoral Research Associate Institute of Biomedical Engineering<http://www.ibme.ox.ac.uk/> Department of Engineering Science University of Oxford Old Road Campus Research Building Oxford, UK OX3 7DQ ________________________________ From: Martin Craig Sent: 25 July 2018 11:38 To: Flora Kennedy McConnell Subject: Re: [FSL] Oxford_ASL - fabber errors. Hi Anthony, Apologies for this. The Centos 6 package has indeed been bundled with an old version of Fabber. I've rebuilt the package for 3.9.15 with the current Fabber and updated it on GitHub - try the new package here: https://github.com/ibme-qubic/oxford_asl/files/2227564/oxford_asl-3.9.15-centos6.tar.gz Please let me know how you get on. I'm not sure why you are getting numerical instability in the spatial step, however it is only affecting a few voxels and the code is supposed to be able to tolerate this and still complete the remainder of the voxels. Cheers, Martin Craig Software developer IBME, Oxford ________________________________ From: Flora Kennedy McConnell Sent: 25 July 2018 11:20:50 To: Martin Craig Subject: Fw: [FSL] Oxford_ASL - fabber errors. Hi Martin, Here is his last email. All the best, Flora Flora Kennedy McConnell ------------------------------ Postdoctoral Research Associate Institute of Biomedical Engineering<http://www.ibme.ox.ac.uk/> 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]<mailto:[log in to unmask]>> on behalf of Anthony Alexander <[log in to unmask]<mailto:[log in to unmask]>> Sent: 24 July 2018 16:18 To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] Oxford_ASL - fabber errors. We are running this on Linux Centos 6 and the output of ./fabber_asl --version is Fabber v3.9.2-78-g7e4027c : Thu Jan 25 13:00:17 2018. Please let me know what else I can provide. Thanks On Tue, Jul 24, 2018 at 7:28 AM, Flora Kennedy McConnell <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Anthony, That's puzzling. Please could you tell me what system (mac or linux distribution) you are using to run the oxford_asl tools? Also, please can you go into the folder where you are storing the downloaded oxford_asl tools and run the command "./fabber_asl --version" and then let me know the output. Thanks, Flora Flora Kennedy McConnell ------------------------------ Postdoctoral Research Associate Institute of Biomedical Engineering<http://www.ibme.ox.ac.uk/> 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]<mailto:[log in to unmask]>> on behalf of Anthony Alexander <[log in to unmask]<mailto:[log in to unmask]>> Sent: 23 July 2018 18:56:09 To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] Oxford_ASL - fabber errors. Hi Flora, Thank you for your response. We are using the newest version of oxford_asl v3.9.15 downloaded from the link you provided. This is running Fabber v3.9.2-78-g7e4027c : Thu Jan 25 13:00:17 2018. Is this not the newest version? If not, I may just have a problem with our paths but it appears to be pulling from the new directory and not our FSL path. Thank you On Mon, Jul 23, 2018 at 11:31 AM, Flora Kennedy McConnell <[log in to unmask]<mailto:[log in to unmask]>> wrote: 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: https://github.com/ibme-qubic/oxford_asl/releases/tag/v3.9.15 This includes a recent version of the fabber_asl executable which should avoid this error. All the best, Flora Kennedy McConnell ------------------------------ Postdoctoral Research Associate Institute of Biomedical Engineering<http://www.ibme.ox.ac.uk/> 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]<mailto:[log in to unmask]>> on behalf of Anthony Alexander <[log in to unmask]<mailto:[log in to unmask]>> Sent: 14 July 2018 00:07:02 To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] Oxford_ASL - fabber errors. Hello 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]<mailto:[log in to unmask]>> 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 Institute of Biomedical Engineering<http://www.ibme.ox.ac.uk/> 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]<mailto:[log in to unmask]>> on behalf of Paul Mullins <[log in to unmask]<mailto:[log in to unmask]>> Sent: 12 July 2018 09:27:40 To: [log in to unmask]<mailto:[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. ######################################################################## 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 ________________________________ 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 ________________________________ 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 ________________________________ 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 ________________________________ 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