2010 Winter Project Week VervetMRILongitudinalAnalysis - Revision history

Fedorov: /* Key Investigators */

2010-01-08T17:34:08Z

Key Investigators

Fedorov: /* Key Investigators */

2010-01-08T16:38:42Z

Key Investigators

Fedorov at 16:03, 8 January 2010

2010-01-08T16:03:44Z

Fedorov at 21:43, 2 January 2010

2010-01-02T21:43:45Z

Fedorov: /* Key Investigators */

2010-01-02T01:00:26Z

Key Investigators

Fedorov: /* References */

2010-01-02T00:59:02Z

References

Fedorov: /* References */

2010-01-02T00:58:34Z

References

Fedorov: /* Key Investigators */

2009-12-22T19:49:19Z

Key Investigators

Fedorov: /* Key Investigators */

2009-12-12T00:45:13Z

Key Investigators

Fedorov: /* Key Investigators */

2009-12-12T00:43:49Z

Key Investigators

@@ Line 74: / Line 74: @@
 * Worked with Kilian / EMSegmenter. Demo of Slicer2 EMSegmenter capabilities, not available in Slicer3. Fine-tuned parameters to achieve very good 3-class segmentation results on one subject.
 * Worked with Daniel / VMTK segmentation to remove vessels prior to segmentation.
+* Discussed the use of additional modalities for segmentation (T2 & PD). Agreed resolution not sufficient to improve results (4 times slice thickness). Single-shot T2/PD DICOM reading issue with Slicer nrrd reader: reported to Xiaodong

@@ Line 18: / Line 18: @@
 * Kilian Pohl (IBM)
 * Hans Johnson (UIowa)
@@ Line 69: / Line 70: @@
 ''During the meeting'':
-* testing and fine-tuning segmentation tools -- ''Work with: EM Segmenter/Kilian Pohl, itkEMS/ABC/Marcel Prastawa''; try to complete segmentation of baseline and followup scans
+* discussed registration with Hans, Martin; looked at atlas to subject registration, confirmed accuracy is good for segmentation
-* improving deformable registration of rhesus atlas to vervet, if needed ([[October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow#Template_Gucci |initial results available]]) ''Work with: Luis Ibanez, Jim Miller, Dominik Maier, Casey Goodlett, Hans Johnson ... any expertise in registration is welcome''
+* Worked with Marcel / ABC segmentation module -- worked out of the box, very few parameters need to be specified. Went through couple of iterations to expose some parameters of ABC (arbitrary number of classes, allow to disable registration, allow to specify priors per class).
-* collect overall comments on the workflow from the related experience in similar workflows (Martin Styner)
+* Worked with Kilian / EMSegmenter. Demo of Slicer2 EMSegmenter capabilities, not available in Slicer3. Fine-tuned parameters to achieve very good 3-class segmentation results on one subject.
 </div>

@@ Line 1: / Line 1: @@
 __NOTOC__
-<gallery perrow="5">
+<gallery perrow="4">
 Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
 Image:Calvin_atlas_demo.jpg | Axial slice for one of the vervet subjects
@@ Line 7: / Line 7: @@
 Image:Calvin_atlas_demo_vervet_gm.jpg | Aligned vervet grey matter probabilistic atlas
 Image:Calvin_atlas_demo_segm.jpg | Overlayed segmentation result by EM Segmenter with vervet probabilistic atlas
 </gallery>
@@ Line 13: / Line 15: @@
 * Andriy Fedorov, Ron Kikinis (BWH)
 * Ginger Li, Chris Wyatt (VT)

@@ Line 3: / Line 3: @@
 <gallery perrow="5">
 Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
-Image:atlas_gm_axial.jpg | GM probabilistic atlas
+Image:Calvin_atlas_demo.jpg | Axial slice for one of the vervet subjects
-Image:atlas_subcortical_models.jpg | Vervet subcortical segmentations
+Image:Calvin_atlas_demo_rhesus_gm.jpg | Aligned rhesus grey matter probabilistic atlas
-Image:Vervet-rhesus-saggital1.jpg | Alignment of rhesus atlas to vervet after affine registration (BRAINSFit)
+Image:Calvin_atlas_demo_vervet_gm.jpg | Aligned vervet grey matter probabilistic atlas
-Image:Vervet-rhesus-saggital2.jpg | Alignment of rhesus atlas to vervet after affine+bspline registration (BRAINSFit)
+Image:Calvin_atlas_demo_segm.jpg | Overlayed segmentation result by EM Segmenter with vervet probabilistic atlas
 </gallery>

@@ Line 61: / Line 61: @@
 * prepared 3-class and subcortical segmentations for one subject (semi-manually)
 * atlas construction workflow is now composed completely from Slicer/NA-MIC Kit tools
-* initial version of the vervet probabilistic atlas completed
+* initial version of the re-worked vervet probabilistic atlas completed
 ''During the meeting'':
 * testing and fine-tuning segmentation tools -- ''Work with: EM Segmenter/Kilian Pohl, itkEMS/ABC/Marcel Prastawa''; try to complete segmentation of baseline and followup scans
-* improving deformable registration of rhesus atlas to vervet ([[October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow#Template_Gucci |initial results available]]) ''Work with: Luis Ibanez, Jim Miller, Dominik Maier, Casey Goodlett, Hans Johnson ... any expertise in registration is welcome''
+* improving deformable registration of rhesus atlas to vervet, if needed ([[October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow#Template_Gucci |initial results available]]) ''Work with: Luis Ibanez, Jim Miller, Dominik Maier, Casey Goodlett, Hans Johnson ... any expertise in registration is welcome''
 * collect overall comments on the workflow from the related experience in similar workflows (Martin Styner)

@@ Line 78: / Line 78: @@
 * [[October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow|Vervet atlas construction workflow]]
 * Relevant papers and studies from UNC:
-** [[DBP2:UNC:Local_Cortical_Thickness_Pipeline#Brain_atlases|UNC Rhesus brain atlase]]
+** [[DBP2:UNC:Local_Cortical_Thickness_Pipeline#Brain_atlases|UNC Rhesus brain atlas]]
 ** [[DBP2:UNC:Cortical_Thickness_Roadmap|Comparison between EM Segmenter and itkEMS]]
 ** M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-

@@ Line 75: / Line 75: @@
 ==References==
-* NA-MIC collaboration page
+* [[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|NA-MIC NCBC Collaboration:Measuring Alcohol and Stress Interaction]]
-* Workflow/progress page
+* [[October_08_2009_Meeting:_VT-NAMIC_Revised_atlas_construction_workflow|Vervet atlas construction workflow]]
-* Relevant papers and studies from UNC
+* Relevant papers and studies from UNC:
-* BRAINSFit registration
+** [[DBP2:UNC:Local_Cortical_Thickness_Pipeline#Brain_atlases|UNC Rhesus brain atlase]]
-* N4 bias correction
+** [[DBP2:UNC:Cortical_Thickness_Roadmap|Comparison between EM Segmenter and itkEMS]]
-* EM Segmenter
+** M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-
-* itkEMS
+** R. C. Knickmeyer, M. Styner, S. J. Short, G. R. Lubach, C. Kang, R. Hamer, C. L. Coe, and J. H. Gilmore, "Maturational trajectories of cortical brain development through the pubertal transition: Unique species and sex differences in the monkey revealed through structural magnetic resonance imaging," pp. bhp166+, August 2009. [http://dx.doi.org/10.1093/cercor/bhp166 DOI]
-* ...
+* [http://www.nitrc.org/projects/multimodereg/ BRAINSFit registration tools (Hans Johnson, UIowa) on NITRC]
 </div>

@@ Line 39: / Line 39: @@
 Alternatively, instead of the Steps 1 and 2 we could use UNC Rhesus atlas, if the structural changes between the rhesus and vervet brains are not significant, and we can successfully perform deformable registration.
-''Question to EM experts: how good should be the alignment between atlas and subject for segmentation?''
+The focus of our work at AHM will be on Step 4 above. Given two types of atlases:
 </div>

@@ Line 33: / Line 33: @@
 '''2.''' Build probabilistic tissue atlas using the baseline images
-'''3.''' Use the atlas and automated segmentation tools to identify subcortical structures in all subjects for the baseline and follow-up scans
+'''3.''' Register follow-up to baseline
 Alternatively, instead of the Steps 1 and 2 we could use UNC Rhesus atlas, if the structural changes between the rhesus and vervet brains are not significant, and we can successfully perform deformable registration.