Saving transformed volumes and segmentations

Support
1

Hello, I have a lot of micro-CT scans that were scanned in different orientations. To get them all in the same orientation for facilitating segmentation, I transform the volumes following this tutorial: https://www.youtube.com/watch?v=GkPHEsB9rOI

We save the transformed data using the resample scalar volume module. When we open these files, they are not aligned in the same way, but rather we have to change the view from “reformat” to “axial” or to “sagittal” etc. This then aligns our data to our desired view.

My question is if there is a way to save the data such that the volume is saved in our desired alignment and we avoid having to change the view once loaded? I have tried saving the file as a .nrrd, .nii.gz, and .tif and none have saved the data in my desired view.

The reason I want to save the data in this specific format is to be able to use Biomedisa to interpolate my segmentations and speed up the segmentation process. Biomedisa uses the original voxel data so the segmentation labels end up not matching the volume.

Alternatively, is there a way to make the segmentations created on the transformed volume match the original voxel data?

Thanks!

2

Hi - Thanks for pointing out the Biomedisa extension - It was discussed here a while ago, but really appears to have progressed a lot.

I didn’t watch the video you linked, but if you apply the same transform to the volume and the segmentation and then harden them, you should be able to save and restore them to nrrd and seg.nrrd file and have them reload in Slicer with the correct overlay because the headers will specify the correct orientation. If you need to change the pixel data you need to use something like the BRAINS Resample module.

1 Like