2008 Summer Project Week:DWI-DTI PrepTools - Revision history

Liuzx at 14:02, 27 June 2008

2008-06-27T14:02:30Z

Liuzx at 13:39, 27 June 2008

2008-06-27T13:39:35Z

Liuzx at 13:38, 27 June 2008

2008-06-27T13:38:50Z

Liuzx at 13:34, 27 June 2008

2008-06-27T13:34:03Z

Styner: /* Key Investigators */

2008-06-16T18:39:35Z

Key Investigators

Styner: /* Key Investigators */

2008-06-16T18:37:47Z

Key Investigators

Styner at 18:35, 16 June 2008

2008-06-16T18:35:32Z

Liuzx at 17:34, 12 June 2008

2008-06-12T17:34:17Z

Liuzx at 17:11, 12 June 2008

2008-06-12T17:11:58Z

Liuzx at 17:08, 12 June 2008

2008-06-12T17:08:00Z

@@ Line 53: / Line 53: @@
 During the 2008 project week:
 * We met with Xiaodong Tao and talked with him the Dicom to nrrd transform and DTI estimation. We will incorporate his Dicom/nrrd format transform work into our pipeline.
-* We met with Casey Goodlett and learned the pipeline to build a DTI atlas and stlas based DTI analysis. Our DWI/DTI preparing tools will run the QC process based on a DTI atlas.
+* We met with Casey Goodlett and learned atlas based DTI analysis. Our DWI/DTI preparing tools will run the QC process based on a DTI atlas.
-* We met Ran Tao from Universith of Utha. We will use their motion/eddy current distortion correction program in our QC pipeline. We also found that extra checking should be performed on the output of this correction procedure, for some of the inferior and superior slices may contain only pieces of brain structures due to the transform for the correction.
+* We met Ran Tao from Universith of Utha. We will use their motion/eddy current distortion correction program in our QC pipeline. We also found that extra checking should be performed on the output of this correction procedure, for some of the inferior and superior slices may contain only pieces of brain structures due to the transform during correction.
 </div>

@@ Line 54: / Line 54: @@
 * We met with Xiaodong Tao and talked with him the Dicom to nrrd transform and DTI estimation. We will incorporate his Dicom/nrrd format transform work into our pipeline.
 * We met with Casey Goodlett and learned the pipeline to build a DTI atlas and stlas based DTI analysis. Our DWI/DTI preparing tools will run the QC process based on a DTI atlas.
-* We met Ran Tao from Universith of Utha. We will use their motion/eddy current distortion correction program in our QC pipeline. We also found that extra checking should be performed on the output of this correction
+* We met Ran Tao from Universith of Utha. We will use their motion/eddy current distortion correction program in our QC pipeline. We also found that extra checking should be performed on the output of this correction procedure, for some of the inferior and superior slices may contain only pieces of brain structures due to the transform for the correction.
 </div>

@@ Line 52: / Line 52: @@
 <h1>Progress</h1>
 During the 2008 project week:
-* We met with Xiaodong Tao and talked with him the Dicom to nrrd transform and DTI estimation. We will incorporate some of his work into our pipeline.
+* We met with Xiaodong Tao and talked with him the Dicom to nrrd transform and DTI estimation. We will incorporate his Dicom/nrrd format transform work into our pipeline.
-* We met with Casey Goodlett and learned the pipeline to build a DTI atlas and stlas based DTI analysis. Our DWI/DTI preparing tools will run the QC process based on an DTI atlas.
+* We met with Casey Goodlett and learned the pipeline to build a DTI atlas and stlas based DTI analysis. Our DWI/DTI preparing tools will run the QC process based on a DTI atlas.
 * We met Ran Tao from Universith of Utha. We will use their motion/eddy current distortion correction program in our QC pipeline. We also found that extra checking should be performed on the output of this correction
-procedure, for some of the inferior and superior slices may contain only pieces of brain structures.
+procedure, for some of the inferior and superior slices may contain only pieces of brain structures due to the transform for the correction.
 </div>

@@ Line 51: / Line 51: @@
 <h1>Progress</h1>
+During the 2008 project week:
 </div>

@@ Line 20: / Line 20: @@
 We are developing a tool for preparing diffusion weighted and diffusion tensor image data.
-Details of the tool functionality were discussed thus far between UNC and Utah. The discussions have been summarized in [[2008_Core_1_UNC_Utah_DTI|it's event page]]:
+Details of the tool functionality were discussed [[2008_Core_1_UNC_Utah_DTI|between UNC and Utah]]:
-* "protocol" based execution via parameter files.
+* "Protocol" based execution
-** Parameter files contain all the settings/preferences/options
+** Parameter files contain all settings
-* Handles the conversion of DICOM data to volumetric image formats (NRRD)
+* Handles conversion of DICOM data to volumetric formats (NRRD)
-* Automated quality control, corrects/rejects data, and provides a reporting facility.
+* Automated quality control, corrects/rejects, provides reporting facility.
-** Motion correction
+* Motion correction
-** Eddy current correction
+* Eddy current correction
-** Interpolation of data
+* Interpolation of data
-** Quality Control
+* Rejection of interslice brightness
-*** Rejection of interslice brightness
+* Local plausibility check with reconstructed DTI
-*** Local plausibility check with reconstructed DTI
+* FA/MD histogram comparison with atlas
-*** FA/MD histogram comparison with atlas
+* Local dot product of principal direction with atlas
-*** Local dot product of principal direction with atlas
+* Full brain tracking for flips/permutations of axes
-*** Full brain tracking for possible flips, permutations of direction axes
+* Focus QC on white matter only
-*** Focus QC on white matter only
+* DTI data, as well as FA/MD

@@ Line 22: / Line 22: @@
 Details of the tool functionality were discussed thus far between UNC and Utah. The discussions have been summarized in [[2008_Core_1_UNC_Utah_DTI|it's event page]]:
-* The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI
+* "protocol" based execution via parameter files.
-* This tool will handle the conversion of DICOM data to volumetric image formats (NRRD) using existing ITK-NAMIC classes
+** Parameter files contain all the settings/preferences/options
-* The tool performs automated quality control, corrects data if possible, possibly rejects parts of the data, and provides a reporting facility. The following functionalities will be supported:
+* Handles the conversion of DICOM data to volumetric image formats (NRRD)
-** Motion correction (using Utah modules)
+* Automated quality control, corrects/rejects data, and provides a reporting facility.
-** Eddy current correction (using Utah modules)
+** Motion correction
-** Interpolation of data, e.g. to upinterpolate to isotropic data
+** Eddy current correction
 ** Quality Control
-*** Rejection of interslice brightness, white or black slice at level of direction images
+*** Rejection of interslice brightness
-*** Local plausibility check with reconstructed DTI. Reject direction image if implausable results
+*** Local plausibility check with reconstructed DTI
 *** FA/MD histogram comparison with atlas
-*** Local dot product of principal direction with atlas,
+*** Local dot product of principal direction with atlas
-*** Full brain tracking to check for possible flips, permutations of direction axes
+*** Full brain tracking for possible flips, permutations of direction axes
-*** Focus QC on white matter only, segment WM from baseline image via Slicer-itkEMS implementation
+*** Focus QC on white matter only
-* Furthermore, DTI data is generated (using Slicer/UNC modules), as well as directly derived images, such as FA/MD etc
+* DTI data is generated, as well as FA/MD etc
@@ Line 59: / Line 59: @@
 </div>
 ===References===

← Older revision		Revision as of 18:35, 16 June 2008
Line 20:		Line 20:
	We are developing a tool for preparing diffusion weighted and diffusion tensor image data.		We are developing a tool for preparing diffusion weighted and diffusion tensor image data.

		+	Details of the tool functionality were discussed thus far between UNC and Utah. The discussions have been summarized in [[2008_Core_1_UNC_Utah_DTI\|it's event page]]:

		+	* The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI
		+	* This tool will handle the conversion of DICOM data to volumetric image formats (NRRD) using existing ITK-NAMIC classes
		+	* The tool performs automated quality control, corrects data if possible, possibly rejects parts of the data, and provides a reporting facility. The following functionalities will be supported:
		+	** Motion correction (using Utah modules)
		+	** Eddy current correction (using Utah modules)
		+	** Interpolation of data, e.g. to upinterpolate to isotropic data
		+	** Quality Control
		+	*** Rejection of interslice brightness, white or black slice at level of direction images
		+	*** Local plausibility check with reconstructed DTI. Reject direction image if implausable results
		+	*** FA/MD histogram comparison with atlas
		+	*** Local dot product of principal direction with atlas,
		+	*** Full brain tracking to check for possible flips, permutations of direction axes
		+	*** Focus QC on white matter only, segment WM from baseline image via Slicer-itkEMS implementation
		+	* Furthermore, DTI data is generated (using Slicer/UNC modules), as well as directly derived images, such as FA/MD etc
		+	* Fltk vs KWWidget: Is Fltk appropriate here?

@@ Line 18: / Line 18: @@
 <h1>Objective</h1>
-We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
+We are developing a tool for preparing diffusion weighted and diffusion tensor image data.
@@ Line 27: / Line 29: @@
 <h1>Approach, Plan</h1>
-Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
+The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI. This tool will handle the conversion of DICOM data to volumetric image formats (NRRD), perform automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.
 </div>
@@ Line 36: / Line 37: @@
 <h1>Progress</h1>
 </div>
@@ Line 46: / Line 46: @@
 ===References===

@@ Line 9: / Line 9: @@
 ===Key Investigators===
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* UNC: Heather Cody Hazlett, Martin Styner, Zhexing Liu
-* Utah: Tom Fletcher, Ross Whitaker
+* Utah: Casey Goodlett, Guido Gerig, Tom Fletcher

@@ Line 6: / Line 6: @@
 __NOTOC__
-===Instructions for Use of this Template===
 ===Key Investigators===