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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]> 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]> on behalf of > Anthony Alexander <[log in to unmask]> > *Sent:* 14 July 2018 00:07:02 > > *To:* [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]> 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]> 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. > > ######################################################################## > > 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