Hi Dan,
Since ERROR 1 is not relevant anymore, can you send the files necessary to reproduce ERROR 2? Make sure the masks are not combined.
I have made some changes to lesion_filling today to catch a few errors more gracefully (it runs some checks on the input files). However theses changes will not be available until the FSL 6.0.2 release. I suspect your ERROR 2 would be caught by some of these new checks, but it would be good to test with your specific input images.
You can upload them using Oxford University’s file sharing service Oxfile: https://oxfile.ox.ac.uk/oxfile/work/extBox?id=71854214AE3B9B40F8
Cheers,
Taylor Hanayik
Taylor Hanayik PhD
Analysis Research Software Engineer
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]
> On 23 Apr 2019, at 18:09, Dan Evans <[log in to unmask]> wrote:
>
> Hi Taylor,
>
> I know that combining the WM and lesion masks is not necessarily the standard way to do it, but I don't think that combining the masks is what is causing the error. At first I was not combining the WM and lesion masks together, but then I was getting a different error (Error #1 below) and it happened for every subject (this also came up in a previous thread about lesion filling). I believe error#1 was due to the fact that the WM mask segmentation was not classifying many of the lesions as part of the WM so when the algorithm went to fill those lesions, they were not included in the WM mask and therefore could not be filled. To get around this I started combining the WM and lesion masks, and that has worked for all of my subjects except for two of them. The strange part about these two subjects is that I get the same error message (Errors #2 & 3 below) whether I combine the WM and lesion masks or not.
>
> ERROR #1
> Read in images
> Counted lesions in mask : total = 1408
> Calculated outer border mask
> Calculated outer border components
> Calculated inner border and region masks
> Component 1 of 1408
> Component 2 of 1408
> Cols = 1 and rows = 41
> Calculating cummulative distribution
> Random sampling...
> Putting samples back into image
> Values are : 263.390015 243.080002 261.850006 261.359985 270.040009 232.960007 245.610001
>
> Image Exception : #4 :: Incompatible number of mask positions and matrix columns
> libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
> Trac_LS_lesfill.sh: line 40: 38604 Abort trap: 6 lesion_filling -i MPRAGE.nii -l ${i}_LL_HRmask.nii.gz -w WM_mask.nii.gz -o ${i}_MPRAGE_filled_FSL.nii.gz -v
>
>
>
> ERROR #2 (WM mask is only WM)
>>> lesion_filling -i Trac006_MPRAGE.nii -l Trac006_LM_thresh_0.4.nii.gz -w sgm_seg_2.nii.gz -o Trac006_test1_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
>
>
> ERROR #3 (WM mask is WM and lesions combined)
>>> lesion_filling -i Trac006_MPRAGE.nii -l Trac006_LM_thresh_0.4.nii.gz -w Trac006_WM_LM_combined.nii.gz -o Trac006_test2_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
>
>
> I hope this information is helpful, please let me know if I can provide any other information that may be of use. Thank you for your help!
>
> Best,
> Dan Evans
> Neuroimaging Manager
> Clinical Neuroscience Lab
> Department of Psychology
> The Ohio State University, Columbus, OH
>
> ########################################################################
>
> 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
