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Freesurfer surface is not aligned to the MR volume #4143

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slicerbot opened this issue Mar 13, 2020 · 5 comments
Open

Freesurfer surface is not aligned to the MR volume #4143

slicerbot opened this issue Mar 13, 2020 · 5 comments
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@slicerbot slicerbot commented Mar 13, 2020

This issue was created automatically from an original Mantis Issue. Further discussion may take place here.

@slicerbot slicerbot added this to the Slicer 4.11.0 milestone Mar 13, 2020
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@pieper pieper commented Mar 25, 2020

Thanks for fixing this @Sunderlandkyl and @lassoan 👍

I the extension ready to go? I don't see it in the extension manager yet and when I load a freesurfer model with a recent nightly it doesn't align with the dicoms. Freesurfer volumes do match.

I know this worked like a decade ago when we first added freesurfer support but this is the first time I've tried in a long time. Were you able to find any documentation about what changed? Was it something in Slicer or Freesurfer?

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@jcfr jcfr commented Mar 25, 2020

For reference, see https://github.com/Sunderlandkyl/SlicerFSImporter (copied from the associated mantis comment)

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@Sunderlandkyl Sunderlandkyl commented Mar 25, 2020

I haven't done much more than some initial implementation in the extension. In the coming weeks, I'll continue to work on it, and move it to the PerkLab organization.

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@pieper pieper commented Mar 25, 2020

Thanks @Sunderlandkyl

I have some data I'd like to get loading properly but it's on a machine where I don't have a slicer build. Should I just look in the code to see what the correction transform is or can you give me some hints?

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@Sunderlandkyl Sunderlandkyl commented Mar 25, 2020

Sure, the FreeSurfer models are positioned so that the origin is at center of the corresponding volume.

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