Operating system: Mac OS X 10.10
Slicer version: 4.6.2
Expected behavior: I import a folder with 421 DICOM slices that should show all of the cranium and mandible of an individual
Actual behavior: The program says that 421 slices have been successfully loaded, when the files of the individual are loaded, the upper part of the cranium is cut out, so it doesn’t show.
Is there a limit of images that can be loaded? How should I solve this problem?? Thank you very much in advance
Thank you very much, I’ve downloaded the newest version of the program and now I realised that the problem is that each individual is comprised of two series of CT scans, I have been looking for an explanation or a tutorial on how to stitch these two sets together but so far I haven’t found anything. Is it possible to do it with Slicer??
EDIT: I’m going to change the name of the topic to make it more accurate
Thanks for the update, it seems we are making progress! Also thanks for changing the title.
Stitching the volumes is possible, but it won’t be trivial. I imagine the major steps will be these:
Make sure the two volumes align. If showing them together (set one as background, the other as foreground with 50% opacity) shows overlap, or the two parts are otherwise do not align, then a transform needs to be created to make them align perfectly (create linear transform in Transforms module, set it to one of the volumes, and tweak the transform until alignment is reached)
Resample the volumes to a common frame of reference. Need to create an empty volume that spans both images, ideally in a way that the voxels do not need to be interpolated. I’d try to do this with the Crop Volume module, but I’m not sure that a ROI larger than the cropped image is handled. Then both volumes need to be resampled to this common frame of reference with Resample Image (BRAINS).
Add the two volumes together with Add Scalar Volumes
The exact details of these steps will need to be figured out. Let us know how it goes.
First of all, thank you again! The thing is that when I load the folder with all of the images Slicer just recognises one patient, and it’s always the same part of the CT scan. I realised the folder contained two different scans because I tried opening the folder in Mimics 10.1, which “made me” choose to load one of the sets.
I’m sorry for all of the trouble, I’m fairly new to using Slicer so I’m still getting used to it
If multiple series are stored in a folder or files of a series is spread across multiple folders then you need to use the DICOM module to import it. It will show you a similar patient/study/series selector as Mimics.
Thank you very much for your answer.
The problem is that it just recognises one patient and shows just one of the halves, whereas Mimics recognises two different sets. I’m still trying to open both halves at the same time to try to stitch both parts together.