NITRC ARCTIC Forum: open-discussion

To Create Cortical Thickness Map

Shan Yang — Wed, 04 Apr 2012 14:07:49 GMT

Hi,

thank you for these useful tools. I was wondering how could I create a cortical thickness map which is not just on boundaries of WM and GM, also inside of GM. I used CortThickCLP. I thought it was the option BvsI? But the results looks very stronge. Could you help me out? Thanks.

Regards,
Shan

RE: CortThick fails w/ error: segmentation fault

Clement Vachet — Fri, 27 May 2011 19:40:22 GMT

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.

CortThick fails w/ error: segmentation fault

binod thapa-chhetry — Mon, 16 May 2011 14:46:19 GMT

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

Welcome to Open-Discussion

Christian Haselgrove — Wed, 10 Dec 2008 23:34:51 GMT

Welcome to Open-Discussion