ProjectWeek200706:ContrastingTractographyMeasures - Revision history

Spujol at 19:00, 15 May 2009

2009-05-15T19:00:18Z

Spujol at 18:51, 15 May 2009

2009-05-15T18:51:55Z

Kikinis: /* This Project's Historical Background */

2008-03-28T16:08:40Z

This Project's Historical Background

Spujol at 22:46, 3 March 2008

2008-03-03T22:46:15Z

Spujol at 22:45, 3 March 2008

2008-03-03T22:45:12Z

RandyGollub at 16:43, 29 January 2008

2008-01-29T16:43:24Z

Spujol at 00:00, 25 January 2008

2008-01-25T00:00:38Z

Spujol at 20:58, 24 January 2008

2008-01-24T20:58:11Z

Spujol at 21:40, 23 January 2008

2008-01-23T21:40:21Z

Spujol at 15:54, 23 January 2008

2008-01-23T15:54:54Z

← Older revision		Revision as of 19:00, 15 May 2009
Line 121:		Line 121:

	[http://www.na-mic.org/Wiki/index.php/AHM_2009:DTI_Breakout AHM 2009 DTI VALIDATION SESSION ]		[http://www.na-mic.org/Wiki/index.php/AHM_2009:DTI_Breakout AHM 2009 DTI VALIDATION SESSION ]
		+
		+	''' Presentation of the preliminary results of the NA-MIC DTI Validation Study ''' at the [http://www.ismrm.org/09/ Annual Meeting of the International Society for Magnetic Resonance in Imaging (ISMRM 2009)]
		+
		+	'Preliminary Results on the use of STAPLE for evaluating DT-MRI tractography in the absence of ground truth.' S. Pujol, C-F. Westin, R. Whitaker, G. Gerig, T. Fletcher, V. Magnotta, S. Bouix, R. Kikinis, W. M. Wells III, and R. Gollub. In Proceedings ISMRM 2009, Apr 18-24, 2009. Honolulu, Hawaii.

← Older revision		Revision as of 18:51, 15 May 2009
Line 119:		Line 119:

	[[DTI_Validation_Telephone_Conferences_2008 \| Notes from the DTI Validation TCons ]]		[[DTI_Validation_Telephone_Conferences_2008 \| Notes from the DTI Validation TCons ]]
		+
		+	[http://www.na-mic.org/Wiki/index.php/AHM_2009:DTI_Breakout AHM 2009 DTI VALIDATION SESSION ]

← Older revision		Revision as of 16:08, 28 March 2008
Line 134:		Line 134:
	== This Project's Historical Background==		== This Project's Historical Background==
	*[[Training:Tractography.Validation \| Tractography Validation]]		*[[Training:Tractography.Validation \| Tractography Validation]]
		+
		+	=Sponsors=
		+	<gallery>
		+	Image:NAMIC 380x463.jpg\|[http://www.na-mic.org National Alliance for Medical Image Computing]
		+	Image:Nac.png\|[http://nac.spl.harvard.edu/nac Neuroimage Analysis Center]
		+	Image:NCIGTlogo.gif\|[http://www.ncigt.org National Center for Image Guided therapy]
		+	Image:LogoBIRN.jpg\|[http://www.nbirn.net/ BIRN]
		+	</gallery>

@@ Line 72: / Line 72: @@
 ** Phantom data: '''tractName_toolName_phantomName_tracts.vtk'''
-''tract1inf_slicerROI_teemPhantom_tracts.vtk
+''tract1inf_slicerROI_teemPhantom_tracts.vtk''
-tract2sup_slicerROI_teemPhantom_tracts.vtk
+''tract2sup_slicerROI_teemPhantom_tracts.vtk''
 ''
 * Each tool developer is responsible for downloading and analyzing the data, optimizing their own algorithm as needed.  Keep careful notes on your final processing methods as you will need to teach them to Sonia Pujol at the Santa Fe retreat.  She will repeat the analysis independently using all the tools herself on the data, these are the result that will be included in summary manuscript(s).

@@ Line 62: / Line 62: @@
 * The second dataset was provided by Randy Gollub and the MIND Clinical Imaging Consortium (MCIC). Cohort includes 10 healthy control subjects scanned twice. Each subject has a 1.5 T DTI scan, structural MRI scans and fMRI scans.
-* Acquisition parameters for both data sets can be found here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/Acquisition Parameters|Acquisition Parameters]].
+* '''Acquisition parameters''' for both data sets can be found here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/Acquisition Parameters|Acquisition Parameters]].
-* The 12 tracts being studied are the cingulum bundle, the uncinate fasiculus, the fornix, the internal capsule, and the arcuate fasiculus on the left and right sides, as well as the corpus callosum ( forceps major and forceps minor).  To see how the first set of ROI's were defined, click here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/ROI_Definitions|ROI Definitions]].
+* The '''12 tracts''' being studied are the cingulum bundle, the uncinate fasiculus, the fornix, the internal capsule, and the arcuate fasiculus on the left and right sides, as well as the corpus callosum ( forceps major and forceps minor).  To see how the first set of ROI's were defined, click here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/ROI_Definitions|ROI Definitions]].
 * Each tool developer is responsible for downloading and analyzing the data, optimizing their own algorithm as needed.  Keep careful notes on your final processing methods as you will need to teach them to Sonia Pujol at the Santa Fe retreat.  She will repeat the analysis independently using all the tools herself on the data, these are the result that will be included in summary manuscript(s).

@@ Line 58: / Line 58: @@
 Details:
-* The first data set was provided by Marek Kubicki.  Cohort includes 5 subjects with schizophrenia and 5 matched healthy controls that are de-identified and not marked as to diagnosis.  Each subject has a 3T high resolution DTI scan, structural MRI scan and expert generated Regions of Interest (ROIs) for each subject that are needed for tract definition.
+* The first data set was provided by Marek Kubicki and used to generate the results for the Santa Fe Workshop.  Cohort includes 5 subjects with schizophrenia and 5 matched healthy controls that are de-identified and not marked as to diagnosis.  Each subject has a 3T high resolution DTI scan, structural MRI scan and expert generated Regions of Interest (ROIs) for each subject that are needed for tract definition. Results from Santa Fe drove the decision to switch to a data set that had two study visits per subject to enable reliability estimates.
 * The second dataset was provided by Randy Gollub and the MIND Clinical Imaging Consortium (MCIC). Cohort includes 10 healthy control subjects scanned twice. Each subject has a 1.5 T DTI scan, structural MRI scans and fMRI scans.
-* Acquisition parameters can be found here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/Acquisition Parameters|Acquisition Parameters]].
+* Acquisition parameters for both data sets can be found here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/Acquisition Parameters|Acquisition Parameters]].
-* The 12 tracts to be studied are the cingulum bundle, the uncinate fasiculus, the fornix, the internal capsule, and the arcuate fasiculus on the left and right sides, as well as the corpus callosum ( forceps major and forceps minor).  To see how the first set of ROI's were defined, click here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/ROI_Definitions|ROI Definitions]].
+* The 12 tracts being studied are the cingulum bundle, the uncinate fasiculus, the fornix, the internal capsule, and the arcuate fasiculus on the left and right sides, as well as the corpus callosum ( forceps major and forceps minor).  To see how the first set of ROI's were defined, click here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/ROI_Definitions|ROI Definitions]].
 * Each tool developer is responsible for downloading and analyzing the data, optimizing their own algorithm as needed.  Keep careful notes on your final processing methods as you will need to teach them to Sonia Pujol at the Santa Fe retreat.  She will repeat the analysis independently using all the tools herself on the data, these are the result that will be included in summary manuscript(s).

← Older revision		Revision as of 21:40, 23 January 2008
Line 104:		Line 104:

	AHM 2008 DTI VALIDATION WORKSHOP [[2008_Winter_Project_Week_Tractography\| AGENDA]] AND [[2008_Winter_Project_Week_Tractography_Meeting_Notes \| MEETING NOTES]]		AHM 2008 DTI VALIDATION WORKSHOP [[2008_Winter_Project_Week_Tractography\| AGENDA]] AND [[2008_Winter_Project_Week_Tractography_Meeting_Notes \| MEETING NOTES]]
		+
		+	[[DTI_Validation_Telephone_Conferences_2008 \| Notes from the DTI Validation TCons ]]
		+

	</div>		</div>

@@ Line 71: / Line 71: @@
 # Volumetric connectivity (Ross Whitaker/Tom Fletcher)
 # [[Projects/Diffusion/Contrasting_Tractography_Measures#GATech|Geodesic Tractography Segmentation]] (Allen Tannenbaum/John Melonakos)
 # GTRACT (Vince Magnotta)
 # Stochastic Tractography (Tri Ngo/Carl-Fredrik Westin)
 In preparation for the upcoming T-con, each algorithm team needs to update this wiki page that describes all the participating [[Projects/Diffusion/Contrasting_Tractography_Measures | tractography algorithms ]] with proposed input and outputs for comparison. UNC and Iowa are done already.