uTIlzReg is for research purposes only and has not been approved for clinical use.
Presentation:
uTIlzReg_Tools is set of helpful tools to treat or analyse nifti images.
Calling the function:
./uTIlzReg_Tools <options>
Options:
ARITHMETIC ON IMAGES:
weightedSum [Nb Images] [Weight1][Image1] [Weight2][Image2]... [Output Image]
> Compute the weighted sum of one or several images
weightedMean [Nb Images] [Weight1][Image1] [Weight2][Image2]... [Output Image]
> Compute the weighted mean of several images
weightedStd [Nb Images] [Weight1][Image1] [Weight2][Image2]... [Output Image]
> Compute the weighted standard deviation between several images
NormGrad [ImageIn][ImageOut]
> Compute the norm of the gradients of [ImageIn] to detect the boundaries. Result is stored in [ImageOut].
IMAGE TREATMENT:
AnisoDiff [ImageIn][ImageOut] [ax][ay][az] [IterationNb][dTau]
> Perform anisotropic diffusion of [ImageIn]. Spatial diffusion parameters are [ax][ay][az] and temporal (iteration more precisely) parameters are [IterationNb][dTau]. Result is stored in [ImageOut].
Diffusion [ImageIn][ImageOut] [IterationNb][dTau] <[Mask][MaskId]>
> Perform isotropic diffusion of [ImageIn]. Spatial diffusion parameter is 1 and temporal (iteration more precisely) parameters are [IterationNb][dTau]. Result is stored in [ImageOut]. If the options <[Mask][MaskId]> are defined, the diffusion is only performed where the intensities of are equal to [MaskId].
Erosion [ImageIn][ImageOut] [IterationNb] <[Mask][MaskId]>
> Erosion of [ImageIn] during [IterationNb] iterations and with a structuring element of 3*3*3 voxels. Result is stored in [ImageOut]. If the options <[Mask][MaskId]> are defined, the erosion is only performed where the intensities of are equal to [MaskId].
Dilation [ImageIn][ImageOut] [IterationNb] <[Mask][MaskId]>
> Dilation of [ImageIn] during [IterationNb] iterations and with a structuring element of 3*3*3 voxels. Result is stored in [ImageOut]. If the options <[Mask][MaskId]> are defined, the dilation is only performed where the intensities of are equal to [MaskId].
PutGLInROI [ImageIn][ImageOut] [Rx1][Rx2][Ry1][Ry2][Rz1][Rz2] [GreyLev]
> Put the grey level [GreyLev] in the ROI defined by [Rx1][Rx2][Ry1][Ry2][Rz1][Rz2] (in voxels)
MaskImage [ImageIn][ImageOut] [Mask][MaskId]
> Apply the mask [Mask] to image [ImageIn]. The values at [MaskId] in [Mask] are set to zero in [ImageOut]
RemoveSmallReg [ImageIn][ImageOut] [IdVoxShape][IdVoxBackG] [MaxSize]
> Put to [IdVoxBackG] the connected sets of voxels of intensity [IdVoxShape] having a size of less than [MaxSize] voxels.
GreyLevThresh [ImageIn][ImageOut] [NewMinGL][NewMaxGL]
> Set to [NewMinGL] all the grey levels under [NewMinGL] and to [NewMaxGL] all the grey levels above [NewMaxGL]. Remark: if [NewMinGL]==[NewMaxGL] a traditional threshold around [NewMinGL] is done instead.
GreyLevResample [ImageIn][ImageOut] [NewMinGL][NewMaxGL]
> Linearly Resample the grey levels between [NewMinGL] and [NewMaxGL].
TREATMENT OF DEFORMATIONS AND IMAGE SPACES:
UnderSample [ImageIn][ImageOut] [factor]
> Undersample the resolution of [ImageIn] with a factor [factor]. The result is saved in [ImageOut].
RegCenterImage [MovingIma][FixedIma][TransfoIma]
> Transform the 'image 2 world' properties of [ImageIn] to be centered on [ImageOut]. Result is in [TransfoIma].
TransfoImag [SourceImage] [DF_X][DF_Y][DF_Z] [TransfoImage]
> Transform the image [SourceImage] using the displacement field [DF_X][DF_Y][DF_Z] (in mm). The transformed image [TransfoImage] is in the D.F. coord. system.
ComposeDispFields [DF1_X][DF1_Y][DF1_Z] [DF2_X][DF2_Y][DF2_Z] [DFC_X][DC1_Y][DC1_Z]
> Compute DispField1 o DispField2 (the displacement fields are in mm / DispFieldComp < coord. sys. of DispField2)
RemAffineContribDF [DFi_X][DFi_Y][DFi_Z] [r_xx r_xy r_xz t_x r_yx ... t_z] [DFo_X][DFo_Y][DFo_Z]
> Suppose [DFi] = (Affine def.) o (Nonaffine def.) > remove the affine contrib [r_xx...] and save the result in [DFo]
ANALYSE IMAGES AND DEFORMATIONS:
SSD [Image1] [Image2] <[Margin]>
> Measure the sum of squared differences and the mutual information between two images
Overlap [Image1] [Image2] [Thresh] <[Margin]>
> Compute de overlap (Dice metric) between two images. In each image, the shape is the grey levels strictly above [Thresh].
Surf_Av_Std_values [RefIma] [Thresh] [Values]
> Mesure the average and std of the intensities in [Values] at the surface of [RefIma] at the threshold [Thresh]
ROI_Av_Std_values [Image] [Rx1][Rx2][Ry1][Ry2][Rz1][Rz2]
> Mesure the average and std of the intensities in the ROI of [Image] defined by [Rx1][Rx2][Ry1][Ry2][Rz1][Rz2]
DispFieldStudy [DefX][DefY][DefZ] <[Mask][MaskID]>
> Quantify the properties of the desiplacement field [DefX][DefY][DefZ]. If the options <[Mask][MaskId]> are defined, the properties are only studied where the intensities of are equal to [MaskId].
CompareLandmarks [Target lm file] [DefX][DefY][DefZ] [Source lm file]
> Measure how the displacement field [DefX][DefY][DefZ] matches the target landmarks [Target lm file] to the source ones of [Source lm file]
