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Hello Dan,

Shapeworks can process volumetric data in mha/nrrdformats. For the NRRD format, the headers are compliant with Teem format(http://teem.sourceforge.net/nrrd/index.html). You can find scripts to save images in this format in MatlabCentral. For the Mha formats, however, no specific header format is required. Below is the header of a typical mha volume we use. Please check if your data matches this format.

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = -58 -190 -319
CenterOfRotation = 0 0 0
AnatomicalOrientation = RAI
ElementSpacing = 1 1 1
DimSize = 103 72 121
ElementSize = 1 1 1
ElementType = MET_INT
ElementDataFile = LOCAL

Hope that helps.

Prateep

On Thu, 11 Sep 2014 16:02:55 +0000
"Leib, Daniel" <leibd@wudosis.wustl.edu> wrote:

Good morning!

I'm hoping to try using ShapeWorks as a means to investigate skull shapes in several different mouse phenotypes, and I can run the tutorials for ShapeWorks just fine, but I'm having trouble getting from my CT scans to an appropriate format.

What I would like to be able to do is go from 16 bit grayscale images generated from Scanco's software, preprocessed in MATLAB, and then written out to the necessary format for ShapeWorksRun, but I can't seem to get any mha or DICOM files with an mhd header to play nice. Are there any examples/documentation on what ShapeWroksRun is explicitly looking for or what header information must be there to run correctly? I've been looking at the ITK documentation and there are so many ways to do things that I'm worried I'm just not doing things in the expected way.

Thanks,

Dan

+++++++++++++++++++++++++++++
Daniel Leib
Department of Orthopaedic Surgery
Musculoskeletal Research Center
Washington University in St. Louis
Office 11506 BJCIH
314-747-2769 Phone
314-362-0334 Fax


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Best
Prateep

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• [shapeworks-users] Getting data into appropriate formats, Leib, Daniel, 09/11/2014
  • Re: [shapeworks-users] Getting data into appropriate formats, prateepm, 09/11/2014
    • RE: [shapeworks-users] Getting data into appropriate formats, Leib, Daniel, 09/11/2014

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