Hi Dan,
Similar to the previous post, it would help to see the images. Could you send the input files you’re passing to “lesion_filling”?
You can upload here:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=690991047F8A89D9F1
At the least, it could be useful to see the output of the fslhd command for each of your input files (to lesion filling) as well. Again, the images would be most helpful in getting this debugged.
Cheers,
Taylor Hanayik
Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]
> On 21 Mar 2019, at 20:02, Dan Evans <[log in to unmask]> wrote:
>
> Hello,
>
> I am getting the same error and have not had any luck solving it yet. Below I have included the verbose output from running the lesion filling command as well as the relevant code I used. Thanks for your help.
>
>
> ERROR MESSAGE:
>
> 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
>
>
>
> RELEVANT CODE:
> #################################################################
> # PURPOSE: This script uses the lesion probability map from the Lesion Segmentation Toolbox to create a binary lesion mask with a user defined threshold.
> # It then uses that mask to fill lesions in the MPRAGE based on a transformation from the LST normalized FLAIR image to MPRAGE space.
> #################################################################
> sublist='Trac003'
> thresh=0.4
>
> for i in $sublist; do
> # filepaths
> #cwd=/Data/TracMRI/LesionSegmentationTesting/pre/${i}
> cd /Data/TracMRI/LesionSegmentationTesting/pre/${i}
>
> # Create binary lesion masks based on LST probability map
> fslmaths ples_lpa_*.nii -thr ${thresh} temp.nii.gz
> fslmaths temp.nii.gz -bin ${i}_LM_thresh_${thresh}.nii.gz
> rm temp.nii.gz
>
> # Register standard space to mprage and output transformation matrix
> flirt -in /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -ref ${i}_MPRAGE_brain.nii.gz -omat standard2highres.mat
>
> # Segment brain extracted MPRAGE and binarize WM mask
> fast -t 1 -n 3 -a standard2highres.mat -o sgm ${i}_MPRAGE_brain.nii.gz
> fslmaths sgm_pve_2.nii.gz -bin WM_mask.nii.gz
>
> # Register LST normalized FLAIR to MPRAGE
> flirt -in mrAxialT2_*.nii -ref MPRAGE.nii -omat mrflair2highres.mat
> flirt -in ${i}_LM_thresh_${thresh}.nii.gz -ref MPRAGE.nii -out ${i}_LL_HRmask.nii.gz -applyxfm -init mrflair2highres.mat -noresampblur
>
> # Fill lesions
> lesion_filling -i MPRAGE.nii -l ${i}_LL_HRmask.nii.gz -w WM_mask.nii.gz -o ${i}_MPRAGE_filled_FSL.nii.gz -v
> done
>
>
>
>
> Best,
> Dan
>
> Daniel G. Evans
> Neuroimaging Manager
> Clinical Neuroscience Lab
> Department of Psychology
> The Ohio State University, Columbus, OH
>
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