Events:VT-NAMIC-NCBC-Collaboration-meeting-2009 - Revision history

Fedorov: /* Progress */

2009-10-09T04:13:39Z

Progress

Fedorov: /* Progress */

2009-10-09T04:12:02Z

Progress

Ginger: /* Progress */

2009-10-09T02:19:49Z

Progress

Fedorov: /* Goals */

2009-10-08T23:10:17Z

Goals

Fedorov: /* Progress */

2009-10-08T19:19:18Z

Progress

Fedorov: /* Progress */

2009-10-08T03:46:38Z

Progress

Fedorov: /* Progress */

2009-10-08T00:48:36Z

Progress

Fedorov: /* Progress */

2009-10-08T00:46:38Z

Progress

Fedorov: /* Progress */

2009-10-08T00:27:58Z

Progress

Fedorov: /* Progress */

2009-10-08T00:23:44Z

Progress

@@ Line 63: / Line 63: @@
 ** Considering the data review (mis-alignment of the subjects in atlas; presense of bias; severe noise problems with some of the subject, while better data is available for the same subjects), and availability of the new tools (BRAINSFit robust up to BSplines, N3 bias correction in Slicer does good job -- can improve bias and registration) agreed that the atlas construction must be revisited
 ** Agreed on the conventions how to choose and load the data, all 10 subjects prepared in NRRD from the raw DICOM data, visually inspected for errors [[October 07 2009 Meeting: VT-NAMIC Data load protocol and comments]]
-** Sandy suggested to include anisotropic diffusion into the atlas construction and segmentation workflow. EM Segmenter result can possibly be improved by adjusting the MFA parameter
+** Sandy suggested to include anisotropic diffusion into the atlas construction and segmentation workflow. EM Segmenter result can possibly be improved by adjusting the MFA parameter.
 ** Ginger's laptop has problems running Slicer -- had to apply updates and are in the process of recompiling Slicer -- should be ready by Thursday
 * Separate page for the [[VT-NAMIC Workflow Slicer-related issues]] -- to be revised and submitted as bug reports

@@ Line 69: / Line 69: @@
 * Oct 8
 ** Work on the revised atlas workflow: [[October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow]]
 ** To be discussed on Oct 9: [[Oct 08 2009 meeting: schedule for Oct 9]]

@@ Line 69: / Line 69: @@
 * Oct 8
 ** Work on the revised atlas workflow: [[October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow]]
 == Attendance ==

@@ Line 20: / Line 20: @@
 *** Potential for cortical thickness measures / integration with Caret or freesurfer
 ** Discuss publication plans
 == Agenda ==

@@ Line 64: / Line 64: @@
 ** Sandy suggested to include anisotropic diffusion into the atlas construction and segmentation workflow. EM Segmenter result can possibly be improved by adjusting the MFA parameter
 ** Ginger's laptop has problems running Slicer -- had to apply updates and are in the process of recompiling Slicer -- should be ready by Thursday
-** TODO: would like to get VPN access to Ginger's workstation at VT to confirm Slicer is installed correctly
+* Separate page for the [[VT-NAMIC Workflow Slicer-related issues]] -- to be revised and submitted as bug reports
 == Attendance ==

@@ Line 59: / Line 59: @@
 * Oct 7
 ** Reviewed available data at the initial time-point: [[October 07 2009 Meeting: VT-NAMIC Data review summary]]
 == Attendance ==

@@ Line 61: / Line 61: @@
 ** The issue with noise in Tommy and Louis resolved: we do not know how the NIFTI images we used before for Tommy and Louis were obtained -- the DICOM data has much better noise characteristics
 {|
 |<gallery perrow="2" heights="200px" widths="300px">
@@ Line 68: / Line 80: @@
 |}
-** Angio sequence (right name?) has apparently been used for some (7 out of 10) subjects
+|}
 {|
 |<gallery perrow="3" heights="300px" widths="800px">
 Image:calvin-angio.jpg|'''Calvin axial showing vessel and volume rendering of vasculature'''
 </gallery>
 |}
-** Strange artifact is observed in the occipital lobe for all subjects. Ron, Sandy, Sota Oguro (SPL radiologist) cannot explain the origin. See Calvin example (note the interpolation is turned off)
+{|
+| '''Strange artifact is observed in the occipital lobe for all subjects. Ron, Sandy, Sota Oguro (SPL radiologist) cannot explain the origin. See Calvin example (note the interpolation is turned off)'''
 {|
 |<gallery perrow="3" heights="200px" widths="300px">
@@ Line 84: / Line 101: @@
 Image:calvin-artefact3.jpg|'''Calvin'''
 </gallery>
 |}
-** Noticeable bias field in the atlas is observed by Ron
+{|
-** Significant mis-alignment of some subjects with the template subject after FLIRT registration is confirmed
+| '''Significant mis-alignment of some subjects with the template subject after FLIRT registration is confirmed'''
-** Ringing artifacts for some (few) subjects
+{|
-** In some sobjects the FOV is axis-aligned, while in others it is tilted. These directions were not preserved in the NIFTI data we were previously using.
+|<gallery perrow="3" heights="200px" widths="300px">
 == Attendance ==