How do I rerun the CSE sequence with an edited mask file

Forums Forums Cortical Surface Extraction How do I rerun the CSE sequence with an edited mask file

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      Hi Im a newbie and working with an uncoventional (non human) dataset. I am interested in generating surface maps of the cortical thickness for my species. I’ve been able to do this succesfully on one specimen using the CSE sequence but I would like to recompute the surface maps using edits made to the mask files.

      I’ve been editing the …cortex.dewisp.mask.nii.gz and saving and applying this but it doesnt seem to be applying my corrections to the white-gray matter border when I rerun the sequence. Which Steps in the SEC sequence should be unchecked if I want the sequence to use the edited dewisp.mask? Or perhaps am I missing something and a few other masks also need to be edited? I am applying a template/atlas brain for my species and have made a label file which seems to be working fine with splitting the hemipsheres and identifying the cerebrum. I’m using the new build for BrainSuite15b.

      Thank you in advance.

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