Allen Brain Atlas in XTK?

Question

How can I render the Allen Brain Atlas (API documentation) in XTK? What format should I use?

score 0 · Answer 1 · edited Jul 10 '13 at 16:40

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MHD format is not natively supported yet, but you can convert the MHD to NRRD or NII using tools such as Slicer4.

edited Jul 10 '13 at 16:40

Charles

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answered Jul 10 '13 at 13:04

Nicolas

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Thanks for the pointer to Slicer4. However, I did not manage to export to a format XTK could process. https://gist.github.com/renaud/5967402 Using the demo download from Slicer4 (Download MRHead), and then save it as VTK, NII, ... – Renaud Jul 10 '13 at 15:45
Yes that's strange there is something funny about those. Does it return any error or display something wrong? – Nicolas Sep 03 '13 at 17:20
No, the display is just blank. I think the export I did does not have the right format (ints, instead of floats, or the other way around). – Renaud Sep 05 '13 at 09:05

score 0 · Answer 2 · answered Aug 31 '15 at 16:20

I like to use c3d for volume format conversion. It supports NRRD files, which I believe XTK can read.

Aside: the Allen Mouse Brain Connectivity Atlas data volumes are served as NRRD files directly. The adult mouse gene expression atlas data volumes are still MHDs, though.

Allen Brain Atlas in XTK?

2 Answers2