Modules:DicomToNRRD-3.6 - Revision history

Matsuij: /* Quick Tour of Features and Use */

2011-03-14T20:27:36Z

Quick Tour of Features and Use

Matsuij: /* Command Line Usage */

2011-03-14T20:15:42Z

Command Line Usage

Matsuij: /* Command Line Usage */

2011-03-14T20:12:45Z

Command Line Usage

Matsuij: /* Command Line Usage */

2011-03-14T20:04:38Z

Command Line Usage

Matsuij: /* Command Line Usage */

2011-03-14T19:48:42Z

Command Line Usage

Matsuij: /* Command Line Usage */

2011-03-14T19:44:32Z

Command Line Usage

Matsuij: /* Source Code and Documentation */

2011-03-14T19:31:48Z

Source Code and Documentation

Taox: /* Supported DWI formats */

2010-12-17T14:00:48Z

Supported DWI formats

Taox: /* Supported DWI formats */

2010-12-09T19:58:38Z

Supported DWI formats

Kikinis: /* Supported DWI formats */

2010-12-09T19:53:24Z

Supported DWI formats

@@ Line 68: / Line 68: @@
 ===Quick Tour of Features and Use===
-[[Image:DicomToNrrd-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
+[[Image:DicomToNrrdConverter_wiki.png|thumb|right|280px|Input/Output panels]]
 When this module is run from Slicer UI, simply select the directories for '''Input Dicom Data''' and '''Output Directory''', enter the filename (without path name, but '''with''' extension, such as '''mydti.nrrd''') in the '''Output Filename''' field, and press "Apply" button.

@@ Line 64: / Line 64: @@
 The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the '''smallGradientThreshold''' flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags.
-'''For Siemens data:''' In event of incorrect metadata for diffusion gradient vector coordinates in the DICOM header public element tags, please set the '''useBMatrixGradientDirections''' flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the '''bMatrix''' DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction vector (column vector) multiplied by the transpose of the unit gradient direction vector. Therefore, for a given gradient direction, the unit gradient direction vector coordinates are the first column of the unitary matrix from a singular value decomposition of its b matrix, while the b value is the trace of its b matrix.
+'''For Siemens data:''' In event of incorrect metadata for diffusion gradient vector coordinates in the DICOM header public element tags, please set the '''useBMatrixGradientDirections''' flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the '''bMatrix''' DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction vector (column vector) multiplied by the transpose of the unit gradient direction vector. Therefore, for a given gradient direction, the unit gradient direction vector coordinates are the first column of the 3x3 unitary matrix from a singular value decomposition of its b matrix, while the b value is the trace of its b matrix.
 ===Quick Tour of Features and Use===

@@ Line 64: / Line 64: @@
 The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the '''smallGradientThreshold''' flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags.
-In event of incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags in '''Siemens data''', please set the '''useBMatrixGradientDirections''' flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the bMatrix DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction (column vector) multiplied by its transpose. Therefore, the gradient direction coordinates and b value of a gradient can be derived from the b matrix elements via singular value decomposition.
+'''For Siemens data:''' In event of incorrect metadata for diffusion gradient vector coordinates in the DICOM header public element tags, please set the '''useBMatrixGradientDirections''' flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the '''bMatrix''' DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction vector (column vector) multiplied by the transpose of the unit gradient direction vector. Therefore, for a given gradient direction, the unit gradient direction vector coordinates are the first column of the unitary matrix from a singular value decomposition of its b matrix, while the b value is the trace of its b matrix.
 ===Quick Tour of Features and Use===

@@ Line 62: / Line 62: @@
   d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr
-The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the smallGradientThreshold flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata diffusion gradient vector coordinate entries in the DICOM header public element tags.
+The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the '''smallGradientThreshold''' flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags.
-In event of incorrect metadata diffusion gradient vector coordinate entries in the DICOM header public element tags for Siemens data, please set the useBMatrixGradientDirections flag.
+In event of incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags in '''Siemens data''', please set the '''useBMatrixGradientDirections''' flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the bMatrix DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction (column vector) multiplied by its transpose. Therefore, the gradient direction coordinates and b value of a gradient can be derived from the b matrix elements via singular value decomposition.
 ===Quick Tour of Features and Use===

@@ Line 62: / Line 62: @@
   d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr
-The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the smallGradientThreshold flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient
+The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the smallGradientThreshold flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata diffusion gradient vector coordinate entries in the DICOM header public element tags.
 ===Quick Tour of Features and Use===

← Older revision		Revision as of 19:44, 14 March 2011
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	d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr		d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr
		+
		+	The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the smallGradientThreshold flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient

	===Quick Tour of Features and Use===		===Quick Tour of Features and Use===

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     --echo
       Echo the command line arguments (default: 0)
     --useIdentityMeaseurementFrame
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       purposes only, the format is not fixed, and will likely change as
       debugging of new dicom formats is necessary. (default: 0)
     --outputVolume <std::string>

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 **Achieva 2.5.3.3
 **Achieva 2.6.1.0
 **Intera 2.1.3.6
 **Intera 2.6.3.5
@@ Line 53: / Line 54: @@
 **SIGNA HDx14.0
 **SIGNA HDxt 15.0
 ====Command Line Usage====

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 **
+====Command Line Usage====
 A command line example for running the module is: