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
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