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arash-n / GBSS

Gray-matter Based Spatial Statistics
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threshold in gbss_2_skel.sh #12

Closed ezefarrher closed 3 years ago

ezefarrher commented 3 years ago

Hi Arash, the threshold in gbss_2_skel.sh, line 139: fslmaths all_fIC_skeletonised -mul mean_GM_skeleton_mask_general -thr 0.65 -bin all_lesion_fIC

does it refer to the same threshold defined in thresh (line 54)? if I choose another threshold, do I need to also change the one in line 139?

Thanks!

arash-n commented 3 years ago

Hi!

This is another threshold. This is supposed to filter out voxels with high fIC (NDI) that have been misclassified as gray matter, etc.

-Arash

arash-n commented 3 years ago

I believe at some point there was an issue with options that I fixed it. As a sanity check, it would be helpful to make sure that the options that you give are passed successfully to the script by adding "echo thresh=$thresh; echo perc=$perc".