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Hi Dan, I’ve looked at the data you sent us and the error is that you have combined your white matter mask and your lesion mask into one file that you are passing in as the white matter mask. You simply need to pass in a lesion mask, a separate white matter mask, and the anatomical image. Don’t combine the lesion and white matter masks into one image. Cheers, Taylor Hanayik Taylor Hanayik PhD Analysis Research Software Engineer FMRIB, John Radcliffe Hospital University of Oxford [log in to unmask]<mailto:[log in to unmask]> On 9 Apr 2019, at 16:14, Dan Evans <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello, I have also encountered this problem, but only in a couple of my subjects. The subjects that throw this error are in the middle of the range of lesion volumes for my sample and lesion filling works for the extremes in the sample. Below is the command I've run and the output I get. lesion_filling -i Trac006_MPRAGE.nii -l Trac006_LM_thresh_0.4.nii.gz -w Trac006_WM_LM_combined.nii.gz -o Trac006_MPRAGE_filled.nii.gz -v Read in images Counted lesions in mask : total = 75 Calculated outer border mask Calculated outer border components Calculated inner border and region masks Component 1 of 75 Component 2 of 75 Component 3 of 75 Cols = 1 and rows = 0 WRONG ASSUMPTION ABOUT MATRIX METHOD IN NEWIMAGE!!!!!! Cols = 1 and rows = 0 Calculating cummulative distribution Random sampling... libc++abi.dylib: terminating with uncaught exception of type NEWMAT::IndexException Abort trap: 6 Thanks for any help! Best, Dan Evans ######################################################################## 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