Hi nileg
Thanks for your response. I have a few doubts.
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When you say you started with the allen brain annotations did you draw these annotations on all slides of the 3d histological/mri volume or only on regularly interspaced one.
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Right now im doing it on regularly interspaced one (draw in illustrator and then extract contours and overlay on the histological image). Then i do an interpolation to propagate the labels to the slices in the middle. However this doesnt preserve the structure boundaries too well and there is some amount of bleeding out of the structure boundaries. And I have to do a fair bit of manual editing on ITK-SNAP. How do you fix this problem. Because the mri volume has over 784 slices in the sagittal section and thats a lot
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After doing these steps i load the segmentation mask in ITK-SNAP and then do an export mesh to get the structure mesh, could you suggest some ways of improving this workflow or some other finer steps that im missing but make the process work much better
Regards
Anurag