ActionPlan - Revision history

RandyGollub at 05:21, 4 October 2007

2007-10-04T05:21:45Z

RandyGollub at 18:03, 2 October 2007

2007-10-02T18:03:43Z

RandyGollub: /* Outcome metrics: */

2007-10-02T17:55:17Z

Outcome metrics:

RandyGollub at 17:54, 2 October 2007

2007-10-02T17:54:23Z

RandyGollub at 17:35, 2 October 2007

2007-10-02T17:35:34Z

RandyGollub at 17:28, 2 October 2007

2007-10-02T17:28:56Z

RandyGollub: New page: Comparative analysis of tractography methods/approaches #General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool #Reproducibility of tractogr...

2007-10-02T16:27:10Z

New page: Comparative analysis of tractography methods/approaches #General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool #Reproducibility of tractogr...

New page

Comparative analysis of tractography methods/approaches
#General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool

#Reproducibility of tractography approaches

#Our same 5 ROIs + CC. Sonia and Randy to make first pass in 1 subject, validate with Marek's lab and then send around to be sure work with algorithms.

Need data sets, appropriate ROIs

Exploration of potential data sets (UNC n=1, 10 acquisitions with 6 directions; MIND n=10, 8 acquisitions, 2x at each of 3 sites with 6 directions and 2x at 1 site with 60 directions).

Sylvain volunteers to make nrrd headers for the 10 MIND subjects data from MGH test/retest with Jeremy, Vince, Randy.

← Older revision		Revision as of 05:21, 4 October 2007
Line 33:		Line 33:

	== Next steps:==		== Next steps:==
−	#T-con November 16th 2 PM EST/ noon MST	+	#T-con November 16th 2 PM EST/ noon MST Agenda items include feedback on sample data set & ROIs
		+	#Next face to face gathering will be at the AHM, Randy to schedule time on the agenda t continue this project
		+	#Proper implementation of DTI gradient orientation system in ITK, nrrd, TEEM, etc (Casey/Tom to file bug report, bring it up in an upcoming Engineering T-con, plan for work on it next Project week))

← Older revision		Revision as of 18:03, 2 October 2007
Line 30:		Line 30:
	#Further discussion of how best to parameterize tracts at January AHM		#Further discussion of how best to parameterize tracts at January AHM
	#		#
		+
		+
		+	== Next steps:==
		+	#T-con November 16th 2 PM EST/ noon MST

@@ Line 28: / Line 28: @@
 #Casey's FiberCompare multiple traceline visualization tool
 #Staple method to find common agreement (specificity and sensitivity)
-#How best to parameterize tracts
+#Further discussion of how best to parameterize tracts at January AHM
+#

@@ Line 21: / Line 21: @@
 #T1 white matter mask co-registered to Eddy current corrected DWI data (NA-MIC affine registration tool) (Freesurfer white matter + ?  vs. EMSegmentation- Sonia/Sylvain)
 #ROIs in DWI/DTI space
 == Outcome metrics: ==
-#Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline) in high resolution.  Use this for test-retest metric
+#Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline).  This will give volumes, overlap, mean and Std Dev of FA, trace, mode.  Use these for test-retest metrics.  Pass these label maps to Sonia she will generate these.

@@ Line 13: / Line 13: @@
 #User interface, hardware/software (processor speed, platform, RAM), operator time
-*Preprocessing stream:
+== Preprocessing stream: ==
-DWI with NiFTY header + gradient directions
+#DWI with NiFTY header + gradient directions
-(Field Map correction (NMN.Iowa.MGH) verify that this is helpful)--
+#Field Map correction (NMN.Iowa.MGH) if we verify that this is helpful
-Eddy Current Correction  (affine registration) (BWH)--
+#Eddy Current Correction  (affine registration) (BWH)
-nrrd (BWH) --
+#nrrd (BWH)
-weighted least squares (FSL won't match on this step) tensor estimation using TEEM library (BWH)--
+#weighted least squares (FSL won't match on this step) tensor estimation using #TEEM library (BWH)
-T1 white matter mask co-registered to Eddy current corrected DWI data (NA-MIC affine registration tool) (Freesurfer white matter + ?  vs. EMSegmentation- Sonia/Sylvain)
+#T1 white matter mask co-registered to Eddy current corrected DWI data (NA-MIC affine registration tool) (Freesurfer white matter + ?  vs. EMSegmentation- Sonia/Sylvain)
-ROIs in DWI/DTI space
+#ROIs in DWI/DTI space
-*Outcome metrics:
-Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline) in high resolution.  Use this for test-retest metric
+== Outcome metrics: ==

@@ Line 1: / Line 1: @@
 Comparative analysis of tractography methods/approaches
 #General Taxonomy (based on ROI requirements)- use all those presented at this conference and FSL tool
 #Reproducibility of tractography approaches
 #Our same 5 ROIs + CC.  Sonia and Randy to make first pass in 1 subject, validate with Marek's lab and then send around to be sure work with algorithms.
-Need data sets, appropriate ROIs
+Need data sets, appropriate ROIs.  Iterate beginning with n=1 for ROI generation.
+Sylvain volunteers to make nrrd headers for the 10 MIND subjects data from MGH test/retest with Jeremy, Vince, Randy.
-Exploration of potential data sets (UNC n=1, 10 acquisitions with 6 directions; MIND n=10, 8 acquisitions, 2x at each of 3 sites with 6 directions and 2x at 1 site with 60 directions).
+*Outcome metrics:
+Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline) in high resolution.  Use this for test-retest metric