Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 - Revision history

Fbudin: /* When Using the module in command line */

2010-12-22T14:46:30Z

When Using the module in command line

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

2010-05-14T21:11:24Z

Quick Tour of Features and Use

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

2010-05-14T21:09:06Z

Quick Tour of Features and Use

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

2010-04-15T18:48:20Z

Quick Tour of Features and Use

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

2010-04-15T18:18:20Z

Quick Tour of Features and Use

Fbudin: /* Examples, Use Cases & Tutorials */

2010-04-14T20:03:25Z

Examples, Use Cases & Tutorials

Fbudin: /* Examples, Use Cases & Tutorials */

2010-04-14T20:01:31Z

Examples, Use Cases & Tutorials

Fbudin: /* Examples, Use Cases & Tutorials */

2010-04-14T20:00:24Z

Examples, Use Cases & Tutorials

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

2010-04-05T14:23:22Z

Quick Tour of Features and Use

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

2010-04-05T14:22:35Z

Quick Tour of Features and Use

@@ Line 106: / Line 106: @@
 ===When Using the module in command line===
 * The Transform can be given through an ITK Transform file. An example is given below.
   #Insight Transform File V1.0

@@ Line 39: / Line 39: @@
 * '''Input/Output:''' Defines input and output files.
-** ''Input volume'' is the volume to resample. It can be either a scalar, a vector or a DW image. '''Be Careful: This module cannot resample DTI'''
+** ''Input volume'' is the volume to resample. It can be either a scalar, a vector or a DW image. '''Be Careful: This module cannot resample DTI, use ResampleDTI instead'''
 ** ''Reference Volume'' (optional) is the volume used to set the sampling parameters (origin, spacing, orientation and dimensions). If it is not set, the input volume will be taken for reference.
 ** ''Output volume'' is the name of the output.

@@ Line 39: / Line 39: @@
 * '''Input/Output:''' Defines input and output files.
-** ''Input volume'' is the volume to resample,
+** ''Input volume'' is the volume to resample. It can be either a scalar, a vector or a DW image. '''Be Careful: This module cannot resample DTI'''
 ** ''Reference Volume'' (optional) is the volume used to set the sampling parameters (origin, spacing, orientation and dimensions). If it is not set, the input volume will be taken for reference.
 ** ''Output volume'' is the name of the output.

@@ Line 48: / Line 48: @@
 * '''Transform Parameters:'''
 ** ''Transform Node'' contains the transform(s) to apply to the image
-** ''Bulk Transform'' allows you, in the case the transform file contains an initialization transform and a BSpline transform, to specify that the initialization transform is part of the BSpline transform. This is, for example, to be used if your transform was computed with BRAINSFit or Deformable BSpline Registration.
+** ''Bulk Transform'' allows you, in the case the transform file contains an initialization transform and a BSpline transform, to specify that the initialization transform is part of the BSpline transform. This is, for example, to be used if your transform was computed with BRAINSFit or Deformable BSpline Registration. This option only works if the BSpline transform is of order 3 (restriction due to the templated implementation of ITK).
 ** ''Transforms Order'' allows the user to tell the module in what order the transforms are stored in the node (or file). Transforms should be backward (from output space to input space). However, in Slicer3, the affine and rigid transform nodes are stored as forward transforms and are inverted when passed to the module.
   Input Image <- Transform0 <- Transform1 <- ... <- Transform n <- Output Image (input-to-output)

@@ Line 48: / Line 48: @@
 * '''Transform Parameters:'''
 ** ''Transform Node'' contains the transform(s) to apply to the image
 ** ''Transforms Order'' allows the user to tell the module in what order the transforms are stored in the node (or file). Transforms should be backward (from output space to input space). However, in Slicer3, the affine and rigid transform nodes are stored as forward transforms and are inverted when passed to the module.
   Input Image <- Transform0 <- Transform1 <- ... <- Transform n <- Output Image (input-to-output)

@@ Line 34: / Line 34: @@
 * The transform can be passed as an ITK Transform file using the command line, or directly as a transform node in Slicer3. In the latter case, the transform can only be rigid or affine.
 * It also allows changing the spacing, the orientation, the size and the origin of the image.
-* '''Be careful''' when applying multiple transforms contained in one file. Pay attention to the order of the transforms in the file. You may also not obtain the same result as other tools would give you. For example, if you register two images using BRAINSFit using an affine and a BSpline transform simultaneously, the output file will contain two transforms. However these two transforms are actually two components of the same transform and should be applied simultaneously. Resample Scalar/Vector/DWI Volume only applies transforms serially. You should therefore not use Resample Scalar/Vector/DWI in this case.
+* '''Be careful''' when applying multiple transforms contained in one file. Pay attention to the order of the transforms in the file. You may also not obtain the same result as other tools would give you. For example, if you register two images using BRAINSFit using an affine and a BSpline transform simultaneously, the output file will contain two transforms. However these two transforms are actually two components of the same transform and should be applied simultaneously. Resample Scalar/Vector/DWI Volume only applies transforms serially. You should therefore not use Resample Scalar/Vector/DWI Volume in this case.
 ===Quick Tour of Features and Use===

@@ Line 48: / Line 48: @@
 ** ''Transform Node'' contains the transform(s) to apply to the image
 ** ''Transforms Order'' allows the user to tell the module in what order the transforms are stored in the node (or file). Transforms should be backward (from output space to input space). However, in Slicer3, the affine and rigid transform nodes are stored as forward transforms and are inverted when passed to the module.
-  Input Image <-> Transform0 <-> Transform1 <-> ... <-> Transform n <-> Output Image (input-to-output)
+  Input Image <- Transform0 <- Transform1 <- ... <- Transform n <- Output Image (input-to-output)
-  Input Image <-> Transform n <-> Transform n-1 <-> ... <-> Transform0 <-> Output Image (output-to-input)
+  Input Image <- Transform n <- Transform n-1 <- ... <- Transform0 <- Output Image (output-to-input)
 * '''Manual Transform:''' if no tranform is set in previous panel, one can enter his own transform
 ** ''Transform Matrix:'' a 12-parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix in column-major order (where the column index varies the fastest), the last 3 are a translation.