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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