Hi,

Thanks for the wonderful software. I was trying to use CortThick to get cortical thickness statistics across different regions using freesurfer parcellation and fsl's FAST segmentation but it quit with the following error message:

binod@soave:~$ CortThickCLP /data/export/home/binod/ARCTIC_trial_50294/used_wmparc_asMASK/cortThick_results --inputSeg /data/export/home/binod/ARCTIC_trial_50294/used_wmparc_asMASK/fast_seg.nii --par /data/export/home/binod/ARCTIC_trial_50294/used_wmparc_asMASK/aparc_a2009s_inT1.nii --WMLabel 3 --GMLabel 2 
WhiteMatterInput: 
GreyMatterInput: 
WhiteMatterLabel: 3
GreyMatterLabel: 2
SegmentationInput: /data/export/home/binod/ARCTIC_trial_50294/used_wmparc_asMASK/fast_seg.nii
Output: /data/export/home/binod/ARCTIC_trial_50294/used_wmparc_asMASK/cortThick_results
WhiteMatterComponentOption: 0
GreyMatterComponentOption: 0
VTKOption: 0
ParcellationOption: /data/export/home/binod/ARCTIC_trial_50294/used_wmparc_asMASK/aparc_a2009s_inT1.nii
ParcellationOption: /data/export/home/binod/ARCTIC_trial_50294/used_wmparc_asMASK/aparc_a2009s_inT1.nii
ParFile: 1
SaveWM: 
SaveGM: 
BoundaryVsInteriorOption: 0
SegImageSize: 74
SegImage: 1

WhiteMatterImageSize: 0
GreyMatterImageSize: 0
SepImage: 0
 Boundary Computation 
 Danielsson Map 
 Calcul Distance
 Hash Map 
 Fin HashMap 
 delete point
Segmentation fault


Can someone please explain what am I doing wrong,please? Thanks in advance.

binod

Dear Binod,

This is surprising, as the command line looks correct. Do the input images look correct? Are the label map and parcellation maps correctly registered to each other?
Otherwise, would it be possible to upload the data somewhere, to try to debug the tool using your data?

Best regards,
Clement.