You can ignore those. They are very quick, low-resolution slices acquired just to see where you are in the scanner and set the field of view for the actual image acquisition.
This is a very special acquisition type, I’m not sure what it can be used for, you can ignore these, too.
All the other volumes are Cartesian volumes acquired with highly-anisotropic spacing, in 3 directions. These kind of acquisitions are optimized for review by humans and not well suited for 3D reconstruction. See detailed explanation here:
You may segment structures in the images using Segment Editor module and generate 3D model. I would recommend to resample the volume to be isotropic (using Crop volume module) before you start segmenting it. You can switch between volumes during segmentation to utilize information in all the volumes.
dont ask me doing it again cause i wont know how haha.
i might be able to paint one by one now… but i believe i am missing the front COR file …never written in the DVD maybe…
i called to the hospital today and tomorrow i might be able to speak with the radiologist in charge of the exporting the files in the dvd… so i will try to get a isotropic sequence even if i have to pay for the DVD again. (the guy i spoke with knows about dicom files to 3d. i was surprised, the future is now… haha… but he wasnt in charge of the magnetic resonance department so couldnt help me. i guess) …
i set 1,1, 15, because that was roughly the distance between scan lines i was able to measure by pixel… was about 14.75 so it was a wild guess…
is this is as good as it gets or i just have gibberish and havent done anything yet? hahaha
First, make sure that you have resampled the volumes to isotropic (cubic voxels in the image instead of elongated boxes). You can do it in the Crop Volumes module).
Since MRI is not the best modality to get an (semi-)automated segmentation of bones, probably it is best if you do it manually. Make sure you name the resample isotropic images so that you can identify them by name. Then right-click one of them in Data module and choose “Segment this…”. Start painting or use any of the tools that you think are convenient. As @lassoan suggest you can switch master volume to make use of image information in the places that have ambiguity. Good luck!