[caret-users] help

[Markus Thuerling]

Dear Sir or Madam,
i am PhD student at the University Duisburg-Essen, Department of Neurology.
I want to show the surface of the nucleus dentatus in the cerebellum with CARET v5.61. My problems are shifts between the anatomical volume (the cerebellum was measured with a SWI sequence, saved as hdr / img-file) and the segmentation volume (the dentatus, saved in a nii-file), the right part of the dentatus (and the same problems with other nucleii) is only saved and i want to color different nucleii.
I used CARET with the following steps:
File\Set Current Directory
File\Open Data File\SWI.hdr as Volume Anatomy File
Create a spec file with structure cerebellum or all and unknown space (are these inormations important?)
Without radiological orientation
File\Open Data File\dentate.nii file as Volume Segmentation File
Change under D/C the Primary Overlay to Segmentation
Volume\Segmentation\Reconstruct into Surface\Solid Structure VTK Model (or Brain Model Surface)
 to get the Surface of the nucleus. This step is problematic, because CARET often shut down (Out of Memory) or don't realise this step. I must often repeat open the Volume Anatomy File to get the Model SURFACE&VOLUME.
The SWI-image file is not correct displayed so i changed the voxel size to 0,5x0,5x0,5mm^3 (the correct voxel size). 
After this step i have a shift between  Anatomy and Segmentation File.
It is possible to color different nucleii?
In the appendix you can find two screenshots. You can see a gray and a red nucleus. When i want to save the files, or use the procedure to the next nucleus, CARET saves ONLY the right nucleus and i can not explain why. 

Thank you in advance Markus Thürling



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