[Nirfast] NIRFASTSlicer Modules

[Scott C. Davis]

Hi Vince,
When that paper was published, the NIRFAST front end (called NIRView) had been built on an older platform (Volview) which has since been deprecated. Over time, it became very difficult to keep the program up to date and functioning on new operating systems, and the platform limited development of new functionality.  In early 2016, we released NIRFASTSlicer to replace the antiquated Volview-based front end.  This version is built on the 3DSlicer platform, a very active open source project whose capabilities continue to grow.  While overall the platform switch has improved stability, functionality and the ability to continue innovative development, some specific functionality available in the pre-Slicer version is not available in the Slicer package. However, developers are working on improved segmentation tools which I expect will be released soon.

To address the specific issue you raise:  Bias correction, skin extraction, and K-means are not available in the NIRFASTSlicer Editor module.  K-means was a semi-auto segmentation process which did a fair job on breast MR images.  Bias correction (basically a high-pass filter for low frequency noise in MR images) and skin extraction were image processing filters applied to the MR images which improved the results of the K-means segmentation.  These are not available in NIRFASTSlicer, however, we have found that the “GrowCut” function applied to breast MRI does a very good job segmenting the tissue without the need for bias correction and skin extraction.  The tutorial should explain how to use this function on breast MR.  

I hope this helps explain.

Best,
Scott


On 10/20/16, 12:58 PM, "Nirfast on behalf of Vincent Kitsmiller" <nirfast-bounces at public.kitware.com on behalf of Vincent.J.Kitsmiller.1 at nd.edu> wrote:

    In reviewing, Fast segmentation and high-quality three-dimensional
    volume mesh creation from medical images for diffuse optical
    tomography, I noticed multiple references to modules which I cannot
    seem to locate in the slicer. I specifically would like to know about
    those from the breast example, seen in the attached picture. If I
    could get some direction on where to find these modules that would be
    wonderful. Thank you.
    
    -Vince Kitsmiller