[GLLUG] Viewing scans

[Phil Weir]

Hi Chris,

On 18/10/15 18:20, Chris Bell wrote:
> Hello,
> I have some CD copies from Imperial College Hammersmith Hospital of CT and MRI
> scans with an included DICOM viewer provided for Windows XP by GE, described
> as suitable for viewing but not diagnostics. I may have up to 10 to view soon.
> The nearly 600MB of data appears to be separate from the viewer, but I have no
> idea how much pre-processing and manipulation was done before the results were
> copied to the CD's. Debian offers the InsightToolKit which appears capable of
> handlng the original machine data, but I have never used it. Any advice?
> Should I just search for a M$ box and use the DICOM viewer?
If you want to view, anonymize, convert, I have found GUI and CLI tools 
on Linux
to be more than adequate (as a dev). In particular, check out Aeskalup 
and GDCM,
both in Ubuntu (and, I expect, Debian) package repositories. For 
something more
in depth, perhaps MITK Workbench (mitk.org) or ITK-SNAP (itksnap.org). 
As you
mentioned, ITK itself has most of the core functionality, in library 
form, and has
Python bindings for scripting (as well as native C++).

For something a bit different: Paraview can actually volume render NifTI 
data,
which Aeskulap can chuck out from DICOM, by turning on a default-disabled
plugin. Check out AnalyzeNifTI in the (not very intuitive) Plugin menu. 
This
may be useful if you want to open segmented surfaces or overlaytext/3D CAD
geometry, or other. If you want to use Paraview for some basic 
post-processing,
I have found applying PointDataToCellData and CellDataToPointData 
filters on
top of each other gives enough blurring of noise to make taking an 
intensity
IsoVolume sort-of-work, but nothing that's going to revolutionize proper
segmentation

With best wishes,

Phil