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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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Pydpiper functionality questions #456

Open araikes opened 3 years ago

araikes commented 3 years ago

Hi all,

@bcdarwin, thanks again for answers on my other question (#455). I have two questions about general functionality from Pydpiper as I look down the line on using this.

  1. Is there an automated way to compute brain volume for ex-vivo brains or is my best option MAGeT + summing ROIs?
  2. We have diffusion data as well that I'm processing with TORTOISE and MRtrix. Is there a Pydpiper/MINC way to get my voted template registered with my DWI data? There was brief mention of multimodal coregistration somewhere in the MICe wiki, but I can't find it offhand.
  3. The test data uses the Dorr 2008 atlas. If I wanted to use the DSURQE atlas and mappings, is the MINC file folder for that sufficient for MAGeT?

Thanks again.

gdevenyi commented 3 years ago
  1. The stats mask + anatGetAll with the Jacobians method on the absolute Jacobians
gdevenyi commented 3 years ago
  1. You can register the average with whatever a structural image looks like from DWI with ants, either converting both to minc or both to nifti, sadly mixing doesn't work right now.
araikes commented 3 years ago

Thanks @gdevenyi