simtk.org

Hello,

Previously I was able to easily add my DICOM files to my project. These were exported to me as basic DICOM files (so each image would consist of a folder of multiple dicom files).
Now I have recieved images exported to me as Enhanced DICOM files, 1 image corresponds with 1 large DICOM file. The MITK DICOM image reader v2 does not work with these as it gives the message as can be seen in the attachment. the MITK simple 3d volume importer does seem to work but only when I try and copy a file into SV, it does not seem to work when I try and add an image into a project (which, ofcourse is neccesary in order to plan path, segmentate etc. ). It seems that when add/replace image in a project is selected, the MITK DICOM image reader v2 is autoselected.
I have already tried to first copy a file into SV with the 3d volume importer and then check the box to apply for future files, but when trying to add an image in the project still auto selects the DICOM image reader v2 and can't load my image into my project.
Could someone please explain to me if it is possible / how to load in these images into projects so I can segmentate them.

Cheers and thanks in advance,
Jack Tattersall

Hi Jack,

SV will not be able to read in a single DICOM file representing an image volume. You will need to to convert the image data into a series of files.

Cheers,
Dave

Hello Jack,

You have two basic options:

1. As Dave suggested, find a DICOM reader that will write the single giant DICOM file into a series of 2-D slices. Perhaps Matlab's image toolkit supports this.

2. Find software that can create a VTK structured grid (i.e. .vti file) from the original DICOM file. You can import this VTK structured grid directly into SV. I don't know if MITK has a VTK export function. I seem to recall that ITK-Snap has one, but I haven't checked recently and I'm not sure it can read your big DICOM file to begin with.

DICOM readers are ultra-sensitive, and the standard is very complex so partial implementations exist everywhere. That's why, if it were me, I'd explore option #2.

Nathan
SimVascular Support Team