Slicer Wiki - User contributions [en]

Modules:ShiftDWIValues-Documentation-3.4

2010-03-30T21:15:34Z

Reckbo:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
__NOTOC__
===Module Name===
Shift DWI values

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Author1: Julien von Siebenthal
* Contact: Ryan Eckbo, PNL, reckbo@bwh.harvard.edu

===Module Description===
Some datasets could contain negative values that generate exceptions in numerical routines. This module shifts values in the positive domain.

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===
Quite easy. Just set the DWI and then click apply.

* '''Input DWI volume:''' set the DWI volume

== Development ==

===Dependencies===

Volumes

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

== More Information ==

===Acknowledgment===
National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (to Ron Kikinis, Marek Kubicki).

===References===

Modules:RecenterScalar2DWI-Documentation-3.4

2010-03-30T21:15:14Z

Reckbo:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
__NOTOC__
===Module Name===
Recenter Scalar to DWI Volume

{|
|[[Image:recenter_1.png|thumb|280px|Before recentering]]
|[[Image:recenter_2.png|thumb|280px|After recentering]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Author: Julien von Siebenthal
* Contact: Ryan Eckbo, PNL, reckbo@bwh.harvard.edu

===Module Description===
ROIs could not be centered correctly on the the DWI volume. This module recenter the ROIs on the associated DWIs.

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===
Quite easy. It is sufficient to select a DWI and a scalar volume (generally a ROI for seeding tractography), then click apply and the correction should be displayed. It is recommended to save the scalar volume afterwards to preserve the correction.

* '''Input DWI volume:''' set the DWI
* '''Input Scalar volume:''' set the associated scalar volume to recenter

== Development ==

===Dependencies===

Volumes

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

== More Information ==

===Acknowledgment===
National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (to Ron Kikinis, Marek Kubicki).

===References===

Modules:StochasticTractography-Documentation-3.4

2010-03-30T21:14:42Z

Reckbo:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
__NOTOC__
===Module Name===
Stochastic Tractography

{|
|[[Image:Cc_01.png|thumb|280px|Corpus callosum with stochastic tractography]]
|[[Image:Cc_stoch.png|thumb|280px|Corpus callosum lateral projections]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: DTI

===Authors, Collaborators & Contact===
* Author: Julien von Siebenthal
* Contributor: Steve Pieper
* Contact: Ryan Eckbo, PNL, reckbo at bwh.harvard.edu

===Module Description===
As a main purpose, the stochastic tractography module helps to evaluate connectivity between two regions of interest (ROIs) of the brain. These ROIs define generally grey matter regions having a specific neurophysiological function. Extensively, study involving more than two regions could still be done by pairing the regions two by two.

To go deeper into learning the module you can download the following [http://www.na-mic.org/Wiki/index.php/Python_Stochastic_Tractography_Tutorial tutorial]

== Usage ==
* You want to study fiber path from a single region of interest (ROI)
* You want to evaluate connectivity between two ROIs

=== Description ===

{|
|[[Image:General.png|thumb|1000px|Stochastic tractography panel]]
|}

With the stochastic tractography module, you can:
{|
|
* Feature 1 : smooth the given Diffusion Weighted Image (DWI) using a Half Width Full Maximum gaussian filter
{|
|[[Image:smooth2.png|thumb|500px|Smoothing step]]
|}
|}

{|
|
* Feature 2 : generate a brain mask from the DWI baseline input
{|
|[[Image:mask2.png|thumb|500px|Brain mask step]]
|}
|}

{|
|
* Feature 3 : create a DTI (Diffusion Tensor Image) tensor from the DWI input
{|
|[[Image:tensor2.png|thumb|500px|Tensor step]]
|}
|}

{|
|
* Feature 4 : produce different measures based on the tensor like fractional anistropy (FA), mode and trace
{|
|[[Image:fa2.png|thumb|500px|Tensor step: FA]]
|[[Image:mode2.png|thumb|500px|Tensor step: mode]]
|[[Image:trace2.png|thumb|500px|Tensor step: trace]]
|}
|}

{|
|
* Feature 5 : produce connection maps in case 2 ROIs are given without ROI filtering from the tractography
** showing union and intersection of both maps from region A to region B and B to A
{|
|[[Image:AorB2.png|thumb|500px|Union of A to B and B to A]]
|[[Image:AandB2.png|thumb|500px|Intersection of A to B and B to A]]
|}
|}

{|
|
* Feature 6 : produce connection maps in case 2 ROIs are given with ROI filtering from the tractography
** showing only tracts connecting region A to region B and B to A
{|
|[[Image:connectAB2.png|thumb|500px|ROI filtering]]
|[[Image:A2B2.png|thumb|500px|ROI filtering from A to B]]
|[[Image:B2A2.png|thumb|500px|ROI filtering from B to A]]
|}
|}

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

{|
|
* '''IO panel:'''
** Input DWI Volume: the DWI is loaded through the Volume module - it is th only mandatory input
** Input ROI Volume (A/B): only 1 ROI is needed to achieve a tractography. If you want to evaluate the connection between two regions, you will give both ROIs
** Input WM Volume: a white matter mask can be given as input to use ones provided by other tools or Slicer modules - it will supersede the brain mask even if enabled. Be mindful in setting a WM: tractography results can be impaired by a too restrictive WM
** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 features just require a DWI
{|
|[[Image:IOmenu.png|thumb|500px|IO step]]
|}
|}

{|
|
* '''Smoothing panel:'''
** Gaussian FWHM: this filter defines a Full Width Half Maximum. You can define it for each direction in modifying each component of the 3-vector
** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
{|
|[[Image:Smoothmenu.png|thumb|500px|Smoothing step]]
|}
|}

{|
|
* '''Brain Mask panel:'''
** Lower/Higher Brain Threshold: this filter is based on a simple level set segmentation - intensities of the baseline lying between the two values will be represented, others are set to 0. The most common use of this filter is to remove ventricles from the tractography domain and most of the outside of the brain
** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
{|
|[[Image:Maskmenu.png|thumb|500px|Brain mask step]]
|}
|}

{|
|
* '''Diffusion Tensor panel:'''
** Important: this step is not mandatory. It is here to evaluate the whole tensor and achieve measurements like FA, mode or trace. You did not need it to achieve tractography
** FA, mode and trace are sent as scalar volumes and inserted in the MRML tree to be further used
** Advice: you can enable solely that functionality and compute several times with different parameters till satisfaction
{|
|[[Image:Tensormenu.png|thumb|500px|Tensor step]]
|}
|}

{|
|
* '''Tractography panel:''' This panel deals with the tractography per se:
** Total tracts: number of generated tracts per voxel
** Maximum tract length (mm): set the maximum length a tract could reach
** Step size (mm): is the step length for the update vector
** Use spacing: must be used with caution - activate spacing of the update vector
** Stopping criteria: FA is used as the stopping criteria. Advice: as ROIs are defined in the grey matter FA are generally very low, therefore do not use it in most cases
{|
|[[Image:Tractomenu.png|thumb|500px|Tractography step]]
|}
|}

{|
|
* '''Connectivity Map panel:''' This panel lets the user modify parameters to create density/connectivity maps. A map is a scalar volume storing the number of times each voxel is traversed by tracts. It can be counted differently which is the purpose of the following parameters:
** Computation mode:
*** binary: voxel counter is incremented by 1 only once
*** cumulative: voxel counter is incremented by 1 each time a tract traverses it
*** weighted: same as cumulative but the increment is the length of the tract traversing the voxel
** Length based: must be enabled if the resulting tracts must be subdivided related to their length ownership
*** dThird: tracts only counted have length between 1 and (maximum tract length)/3
*** mThird: tracts only counted have length between (maximum tract length)/3 and 2 * (maximum tract length)/3
*** uThird: tracts only counted have length between 2 * (maximum tract length)/3 and (maximum tract length)
*** vicinity: in case of 2 ROIs connectivity assessment, setting vicinity to a positive value creates a neighborhood (in voxels) around the ROIs. This could help in counting tracts that ternminate near the ROIs but not accurately in
*** threshold: defines the connection probability under which tracts are rejected
{|
|[[Image:Connectmenu.png|thumb|500px|Connectivity step]]
|}
|}

== Development ==

===Dependencies===

Volumes

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

== More Information ==

===Acknowledgment===
National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (to Ron Kikinis, Marek Kubicki).

===References===
* [http://lmi.bwh.harvard.edu/papers/pdfs/2002/bjornemoMICCAI02.pdf Björnemo M, Brun A, Kikinis R, Westin CF. Regularized stochastic white matter tractography using diffusion tensor MRI. In Fifth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'02). Tokyo, Japan, 2002;435-442.]
* [http://lmi.bwh.harvard.edu/papers/pdfs/2006/frimanTMI06.pdf Friman, O., Farneback, G., Westin CF. A Bayesian Approach for Stochastic White Matter Tractography. IEEE Transactions on Medical Imaging, Vol 25, No. 8, Aug. 2006]
* [http://www.na-mic.org/Wiki/index.php/Image:IC_posternew.png Shenton, M.E., Ngo, T., Rosenberger, G., Westin, C.F., Levitt, J.J., McCarley, R.W., Kubicki, M. Study of Thalamo-Cortical White Matter Fiber Tract Projections in Schizophrenia Using Diffusion Stochastic Tractography. Poster presented at the 46th Meeting of the American College of Neuropsychopharmacology, Boca Raton, FL, December 2007.]

Modules:ResampleDTIVolume-Documentation-3.4

2010-03-30T21:14:15Z

Reckbo:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
__NOTOC__
===ResampleDTIVolume===

{|
|[[Image:Slicer3_-_ResampleDTIVolume_Module_menu.png|thumb|280px|Module Panel]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Diffusion Tensor

===Authors, Collaborators & Contact===
* Francois Budin
* Sylvain Bouix, PNL
* Contact: Ryan Eckbo, PNL, reckbo[at]bwh[dot]harvard[dot]edu

===Module Description===
This module implements Diffusion Tensor Image (DTI) resampling through the use of ITK Transforms. It supports any transform that is implemented in ITK (rigid, affine, non-rigid such as BSpline, etc). 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is especially appropriate when one needs to resample an image and already knows the transform to apply to it. Its principal advantages resides in the fact that one can apply any kind of transform supported by ITK (rigid, affine and non-rigid) and can choose between the most commonly used interpolators.
* 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. In that case, the image will be modified in consequences.

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

* '''Input/Output:''' Defines input and output files.
** ''Input volume'' is the volume to resample,
** ''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.
* '''Resampling Parameters:'''
** ''Number Of Threads'' sets the number of threads used to perform the resampling.
** ''Correction'' sets if a filter is applied on the resampled image to ensure that every tensor is positive definite symmetric. Three filters are available: set to zero the negative eigen values, take their absolute values or compute their closest positive definite symmetric matrix.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, one can select it here.
* '''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.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' It should normally not be modified when using this module directly in Slicer3 with a transform node. It does not specify whether the matrix is expressed in LPS or RAS coordinate space but rather if everything is expressed in the same coordinate space. LPS means that everything is in the same space and RAS means that it is not the case. This option can be set to RAS if the given transform is in RAS coordinate space (respectively LPS) and the input volume is in LPS coordinate space (respectively RAS). '''Be careful''': When passing manually the transform, the coordinate space modification is directly applied on the given transform. However, when passing the transform through a file or a transform node, it is the input volume coordinate space that is modified and the transform is left unchanged (so that any kind of transform supported by ITK is also supported by this module). If one sets the output volume parameters manually, one has to pay attention to the fact that in that case the given parameters are considered to be in the transform coordinate space!!!
* '''Rigid/Affine Parameters:'''
** ''Rotation Point:'' uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.
** ''Centered Transform:'' sets the center of the transformation to the center of the image.
** ''Inverse ITK Transformation:'' inverses the transformation before applying it to the image. The transform given to the module is from the output image to the input one. If one wants to specify a transform from the input image to the output image, one should use this flag. This option can only be used if the transform is rigid or affine. Be careful: if the file containing the transform contains multiple transforms, only rigid and affine transforms will be inverted.
* '''Affine Transformation Type:''' Use the Preservation of the Principal Direction (right image) to compute the affine transform. Otherwise, the Finite Strain Method (left image) is used [[#References|[1] ]].

{|
|[[Image:320px-Plan2dyz-skew-noppd-vertical.jpg|thumb|250px|Finite Strain]]
|[[Image:320px-Plan2dyz-skew-ppd-vertical.jpg|thumb|250px|Preservation Of Principal Direction]]
|}

* '''Interpolation Type:''' sets the type of interpolation kernel to either linear, nearest neighbor (nn), windowed sinc (ws), or b-spline (bs). The windowed sinc interpolator uses a constant boundary condition whereas the b-spline interpolator uses a mirror boundary condition.
* '''Windowed Sinc Interpolate Function Parameters:''' selects the type window function for the sinc interpolation h=hamming, c=cosine, w=welch, l=lanczos, b=blackman. '''This is only relevant if one selects ws as the interpolation type'''.
* '''BSpline Interpolate Function Parameters:''' The spline order (only relevant if the selected interpolator is bs).
* '''Output Parameters:''' One can overwrite the reference volume parameters by setting manually the ''spacing'', ''size'', ''origin'' (as a fiducial), and ''direction matrix'' (also known as space directions) in column-major order.

== Development ==

===Dependencies===

None

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/ link] to ResampleDTIVolume.

== More Information ==

===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
# Transform 0
Transform: AffineTransform_double_3_3
Parameters: 1.73205080756880 0.5 0 -0.5 .8660254037844 0 0 0 1.5 15 32 27
FixedParameters: 40 35 20

* '''Be Careful :''' The transform file must have an empty line after the fixed parameters
* The Fixed Parameters are the coordinates of the center of rotation
* The Parameters are written in the following format:
** 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.
* A transform file may contain multiple transforms. The module will apply all of them.

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics].

===References===
[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".

[1] D.C. Alexander, C. Pierpaoli, P.J. Basser, J.C. Gee. Spatial Transformations of Diffusion Tensor Magnetic Resonance Images, IEEE Transactions on medical imaging, vol. 20, No. 11, November 2001

Modules:ResampleScalarVectorDWIVolume-Documentation-3.6

2010-03-30T21:13:43Z

Reckbo:

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Resample Scalar/Vector/DWI Volume===

{|
|[[Image:ResampleVolume2Modulewithpanelsexpanded.png|thumb|280px|Module with panels expanded]]
|[[Image:OriginalBrainWebImage.jpg|thumb|200px|Original Image [[#References|[1] ]] ]]
|[[Image:BrainWebImageTransformed.jpg|thumb|200px|Transformed Image]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Francois Budin, NIRAL
* Sylvain Bouix, PNL
* Contact: Ryan Eckbo, PNL, reckbo[at]bwh[dot]harvard[dot]edu

===Module Description===
Resampling consists in applying a transformation to an image, usually to align it with other images to be able to compare them. This module implements image and vector-image resampling through the use of ITK Transforms. It supports any transform that is implemented in ITK (rigid, affine, non-rigid such as BSpline, etc). It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is especially appropriate when one needs to resample an image and already knows the transform to apply to it. Its principal advantages resides in the fact that one can apply any kind of transform supported by ITK (rigid, affine and non-rigid) and can choose between the most commonly used interpolators.
* 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.

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

* '''Input/Output:''' Defines input and output files.
** ''Input volume'' is the volume to resample,
** ''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.
* '''Deformation Field:''' Allows the user to transform the input image using a deformation field. The deformation field is applied last in the case other transforms are given.
** ''Displacement or H- field'' sets the type of deformation field. An H-field contains at each voxel the position in space of the transformed point. The displacement field contains at each voxel the displacement vector to apply to this point.
** ''Deformation Field Volume'' sets the deformation field. It should be a 3-Dimensional vector image. Vectors should be of dimension 3.
* '''Resampling Parameters:''' Sets the number of threads used to perform the resampling.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, one can select it here.
* '''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.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' It should normally not be modified when using this module directly in Slicer3 with a transform node. It does not specify whether the matrix is expressed in LPS or RAS coordinate space but rather if everything is expressed in the same coordinate space. LPS means that everything is in the same space and RAS means that it is not the case. This option can be set to RAS if the given transform is in RAS coordinate space (respectively LPS) and the input volume is in LPS coordinate space (respectively RAS). '''Be careful''': When passing manually the transform, the coordinate space modification is directly applied on the given transform. However, when passing the transform through a file or a transform node, it is the input volume coordinate space that is modified and the transform is left unchanged (so that any kind of transform supported by ITK is also supported by this module). If one sets the output volume parameters manually, one has to pay attention to the fact that in that case the given parameters are considered to be in the transform coordinate space!!!
* '''Rigid/Affine Parameters:'''
** ''Rotation Point:'' uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.
** ''Centered Transform:'' sets the center of the transformation to the center of the input image.
** ''Inverse ITK Transformation:'' inverses the transformation before applying it to the image. The transform given to the module is from the output image to the input one. If one wants to specify a transform from the input image to the output image, one should use this flag. This option can only be used if the transform is rigid or affine.
* '''Interpolation Type:''' sets the type of interpolation kernel to either linear, nearest neighbor (nn), windowed sinc (ws), or b-spline (bs).
* '''Windowed Sinc Interpolate Function Parameters:''' selects the type window function for the sinc interpolation h=hamming, c=cosine, w=welch, l=lanczos, b=blackman. '''This is only relevant if one selects ws as the interpolation type'''.
* '''BSpline Interpolate Function Parameters:''' The spline order (only relevant if the selected interpolator is bs).
* '''Output Parameters:''' One can overwrite the reference volume parameters by setting manually the ''spacing'', ''size'', ''origin'' (as a fiducial), and ''direction matrix'' (also known as space directions) in column-major order.

== Development ==

===Dependencies===

The module uses some source code present in the ResampleDTI module repository.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/ResampleVolume2.cxx ResampleVolume2.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/ResampleVolume2.xml ResampleVolume2.xml ]

Source code from ResampleDTI used in this module too:

*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/itkWarpTransform3D.h itkWarpTransform3D.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/itkWarpTransform3D.txx itkWarpTransform3D.txx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/itkTransformDeformationFieldFilter.h itkTransformDeformationFieldFilter.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/itkTransformDeformationFieldFilter.txx itkTransformDeformationFieldFilter.txx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/dtiprocessFiles/deformationfieldio.h deformationfieldio.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/dtiprocessFiles/deformationfieldio.cxx deformationfieldio.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/dtiprocessFiles/dtitypes.h dtitypes.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/dtiprocessFiles/itkHFieldToDeformationFieldImageFilter.h itkHFieldToDeformationFieldImageFilter.h ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/DiffusionApplications/ResampleDTI/dtiprocessFiles/itkHFieldToDeformationFieldImageFilter.txx itkHFieldToDeformationFieldImageFilter.txx ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1WarpTransform3D.html WarpTransform3D ]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1TransformDeformationFieldFilter.html TransformDeformationFieldFilter ]
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1HFieldToDeformationFieldImageFilter.html HFieldToDeformationFieldImageFilter ]

== More Information ==

===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
# Transform 0
Transform: AffineTransform_double_3_3
Parameters: 1.73205080756880 0.5 0 -0.5 .8660254037844 0 0 0 1.5 15 32 27
FixedParameters: 40 35 20

* '''Be Careful :''' The transform file must have an empty line after the fixed parameters
* The Fixed Parameters are the coordinates of the center of rotation
* The Parameters are written in the following format:
** 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.
* A transform file may contain multiple transforms. The transforms are all merged together before being applied to the image. Therefore the interpolation operation is performed only once per voxel which improves the quality of the output image compared to applying each transform separatly. The transforms are applied in the following order:
Input Image -> Transform0 -> Transform1 -> ... -> Transform n -> Output Image

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics].

===References===
[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".

[1] [http://www.bic.mni.mcgill.ca/brainweb/ BrainWeb: Simulated Brain Database]