CIBC:Documentation:SCIRun:Reference:Teem:TendEpireg
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TendEpireg
Information
- Package: Teem
- Catagory: Tend
- Author(s): Martin Cole
- Status: Supported in latest version
- Version: 3.0
Description
Summary
Register diffusion-weighted echo-planar images.
Detailed Description
Register diffusion-weighted echo-planar images. This registration corrects the shear, scale, and translate along the phase encoding direction (assumed to be the Y (second) axis of the image) caused by eddy currents from the diffusion-encoding gradients with echo-planar imaging. The method is based on calculating moments of segmented images, where the segmentation is a simple procedure based on blurring (optional), thresholding and connected component analysis. The registered DWIs are resampled with the chosen kernel, with the seperate DWIs stacked along axis 0.
List of Gradients : List of gradients, one gradient per line.
Reference :which of the DW volumes (zero-based numbering) should be used as the standard, to which all other images are transformed. Using -1 means that 9 intrinsic parameters governing the relationship between the gradient direction and the resulting distortion are estimated and fitted, ensuring good registration with the non-diffusion-weighted T2 image (which is never explicitly used in registration). Otherwise, by picking a specific DWI, no distortion parameter estimation is done. This value should be an integer.
Blur X :standard devs in X direction of gaussian filter used to blur the DWIs prior to doing segmentation. This blurring does not effect the final resampling of registered DWIs. Use 0.0 to indicate no blurring This value should be a float.
Blur Y :standard devs in Y direction of gaussian filter used to blur the DWIs prior to doing segmentation. This blurring does not effect the final resampling of registered DWIs. Use 0.0 to indicate no blurring This value should be a float.
Threshold : Threshold value to use on DWIs, to do initial seperation of brain and non-brain. If the Use Default Threshold checkbox is checked, the threshold is determined automatically by histogram analysis.
CC Analysis : Use connected component analysis, after thresholding and before moment calculation. Doing connected components analysis usually gives better results because it converts the thresholding output into something much closer to a real segmentation.
Fitting : Only meaningful when the Reference equals -1. hen doing linear fitting of the intrinsic distortion parameters, it is good to ignore the slices for which the segmentation was poor. A heuristic is used to rank the slices according to segmentation quality. This option controls how many of the (best) slices contribute to the fitting. Use 0 to disable distortion parameter fitting. This value should be a flot.
Kernel : kernel for resampling DWIs along the phase-encoding direction during final registration stage.
Sigma : sigma used when kernel is gaussian.
Extent : extent used when kernel is gaussian.
Frequently Asked Questions
Known Bugs
Recent Changes
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