Modules:BRAINSResample

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Module Name

BRAINSResample

User Interface

General Information

Module Type & Category

Type: CLI

Category: Registration

Authors, Collaborators & Contact

• Author1: Hans Johnson, University of Iowa
• Contributor1: Kent WIlliams, University of Iowa
• Contact: Hans Johnson, hans-johson at uiowa.edu

Module Description

BRAINSResample is a program whose purpose is to resample image volumes to a new resolution, optionally applying a transformation.

Usage

BRAINSResample collects together three common image processing tasks that all involve resampling an image volume: Resampling to a new resolution and spacing, applying a transformation (using an ITK transform IO mechanisms) and Warping (using a vector image deformation field).

Quick Tour of Features and Use

Input Image Files Image To Warp: Input Image to transform/warp Reference Image: Defines the output space into which Image will be warped Deformation Field: Vector volume defining voxel transformation Warping Parameters Warp By Transform: Filename of BRAINSFit Transfrom file to use in place of deformation field Pixel Type: Specifies pixel type for input & output image. "binary" pixel type uses a modified algorithm whereby the image is read as unsigned char voxels, a signed distance map is created, te signed distance map is resampled, and the thresholded image is written to disk. Interpolation Mode: Specifies which interpolator is used. Invert Linear Transform: Perform transform inversion in ITK physical space before applying linear transform to the image. Result File Output Image: the input image, transformed/warped and then resampled into the reference image space.

User Interface

Development

Dependencies

BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.

Tests

TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.

Known bugs

Links to known bugs in the Slicer3 bug tracker

• Bug 000: description

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

<!== ===Source code & documentation===

Links to the module's source code:

Source code:

• file.cxx
• file.h

Doxygen documentation:

• class1

More Information

List of all parameters

  --outputVolume <std::string>
    Resulting deformed image

  --useTransformMode <std::string>
    This defunct parameter is no longer in service.  Now ApplyWarp infers
    the transform type from the contents of the .mat file.

  --defaultValue <float>
    Default voxel value (default: 0)

  --invertTransform
    Perform transform inversion in itk physical space before applying the
    linear transform to the image. (default: 0)

  --interpolationMode <NearestNeighbor|Linear|BSpline|WindowedSinc>
    Type of interpolation used (default: Linear)

  --pixelType <uchar|short|ushort|int|uint|float|binary>
    Specifies the pixel type for the input/output images.  The 'binary'
    pixel type uses a modified algorithm whereby the image is read in as
    unsigned char, a signed distance map is created, signed distance map
    is resampled, and then a thresholded image of type unsigned char is
    written to disk. (default: uchar)

  --warpTransform <std::string>
    Filename for the BRAINSFit transform used in place of the deformation
    field

  --deformationVolume <std::string>
    Deformation Field

  --referenceVolume <std::string>
    Reference image defining the output space

  --inputVolume <std::string>
    Image To Warp

Acknowledgment

Include funding and other support here.

References

Publications related to this module go here. Links to pdfs would be useful. -->