Hi, I’m Eiichi, a Japanese plastic surgeon and researcher.
I am studying the evaluation of the healing process of cranial bone defects in rats.
For this purpose, the cranial crowns of rats are collected and imaged with μCT.
I am trying to perform 3D segmentation using a slicer, but the scale of sagittal/coronal is not correct and it does not work well.
Is this a problem that can be solved by manipulating the slicer? Or should I use software other than slicer?
Apologies that this is an out of place question.
Thanks.
What you experienced is quite common with μCT images, as these scanners often create invalid DICOM files or export data in non-standard formats.
If you provide us more information about your scanner, the used file format, and preferably also provide a sample data set (upload to dropbox/onedrive/google drive and post the link here) then we may give some tips about how to fix your data.
It seems that ITK (the library that Slicer uses for reading/writing images) recognizes this file format but it cannot determine the distance between slices. However, often micro-CT scans are acquired with isotropic spacing, and it seems to be the case here, too. So, you can fix the loaded image by manually setting in Volumes module the slice spacing (spacing along the third image axis) from 1.0 to the same value as the spacing along the first two image axes:
