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

In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

Acknowledgment

Include funding and other support here.

References

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