From Vincent.J.Kitsmiller.1 at nd.edu Thu Oct 20 12:58:50 2016 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Thu, 20 Oct 2016 12:58:50 -0400 Subject: [Nirfast] NIRFASTSlicer Modules Message-ID: 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2016-10-20 at 12.55.23 PM.png Type: image/png Size: 73155 bytes Desc: not available URL: From h.dehghani at cs.bham.ac.uk Fri Oct 21 03:26:41 2016 From: h.dehghani at cs.bham.ac.uk (Hamid Dehghani) Date: Fri, 21 Oct 2016 08:26:41 +0100 Subject: [Nirfast] NIRFASTSlicer Modules In-Reply-To: References: Message-ID: <568ac817-81d8-2358-0ba1-4306b5ec83ce@cs.bham.ac.uk> These were part of the now defunct NirView. NIRFASTSLicer has components of these, but the examples given in the tutorial is all that we have currently. On 20/10/2016 17:58, Vincent Kitsmiller 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 > > > > _______________________________________________ > Nirfast mailing list > Nirfast at public.kitware.com > http://public.kitware.com/mailman/listinfo/nirfast > -- -------------------------- Hamid Dehghani, PhD, MIPEM School of Computer Science Acting Director, Physical Sciences for Health Doctoral Training Centre University of Birmingham B15 2TT 0121 414 8728 https://www.cs.bham.ac.uk/~dehghanh/mi-lab.html From Vincent.J.Kitsmiller.1 at nd.edu Wed Oct 26 11:16:40 2016 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Wed, 26 Oct 2016 11:16:40 -0400 Subject: [Nirfast] NIRFASTSlicer Modules In-Reply-To: <9A283144-567F-4A76-93CE-F25AB8B06AC2@dartmouth.edu> References: <9A283144-567F-4A76-93CE-F25AB8B06AC2@dartmouth.edu> Message-ID: Thanks for the response. I then have a follow up question. I have a set of tifs from an MRI. It has been segmented into two regions and saved as two sets of greyscale and RGB tif files (fibroglandular greyscale and RGB, adipose greyscale and RGB). Is there a way to create a region segmented mesh from this data? Thanks. -Vince On Wed, Oct 26, 2016 at 10:23 AM, Scott C. Davis wrote: > 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" 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 > > From Scott.C.Davis at dartmouth.edu Wed Oct 26 10:23:53 2016 From: Scott.C.Davis at dartmouth.edu (Scott C. Davis) Date: Wed, 26 Oct 2016 14:23:53 +0000 Subject: [Nirfast] NIRFASTSlicer Modules In-Reply-To: References: Message-ID: <9A283144-567F-4A76-93CE-F25AB8B06AC2@dartmouth.edu> 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" 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