I am having issues with generating a smooth segment with sufficient enough resolution to serve my purposes. I have a skull scanned in a medical setting. The Volumes module reports the dimensions are 512x512x44 and the spacing is 0.488281mm x 0.488281mm x 5mm. Based on similar support threads, this seems to be related to the fact that this is anisotropic (?). I have found support threads that seem to indicate that this may be an intrinsic property of the scan related to common radiology strategies to reduce radiation/scan time, but (unfortunately for me) results in an anisotropic scan which is not useful for segmentation purposes in 3Dslicer. Here is my question:
Can one somehow fix this problem by using the “Resample Scalar Volume” module and/or the “Crop Volume” module (or some other technique)? Based on feedback on a similar thread, I attempted using the Crop Volume module, selecting “Isotropic spacing” and “B-spline” (this resulted in spacing: 0.48mmx0.48mmx0.48mm & dimensions: 512x512x450), but unfortunately the resulting segment is still isn’t great (see green segment).
I really enjoy using 3DSlicer and I have found there to be many potential research opportunities using patient scans; however, I frequently find this to be a hurdle in obtaining segments which are morphologically accurate enough for research purposes. I suppose for scans that I acquire myself I can simply request an isometric scan(?); however, this may not help with other databases of patient scan data.
Any help or advice would be very greatly appreciated. Also, I would be very interested in learning more from resources which go into further detail on this subject so I can develop better strategies for scan acquisition and/or scan processing prior to segmentation etc. THANK YOU SO MUCH