Image Processing Software#
To smooth an image choosing the dimension(s) in which you want to apply the smoothing
c3d <input_image> -smooth <std_dim1>x<std_dim2>x<std_dim3>vox -o <output_image>
where <std_dim1>, <std_dim2> and <std_dim3> are the standard deviation of the Gaussian kernel in each dimension.
c3d t2.nii.gz -smooth 0x0x5vox -o t2_z_smoothed.nii.gz
Smooth the image t2.nii.gz only along the third dimension with a standard deviation of 5 voxels in this dimension.
c3d t2.nii.gz -smooth 1vox -o t2_smoothed.nii.gz
Smooth the image t2.nii.gz in every direction with a standard deviation of 1 voxels.
The median filter, contrary to the gaussian filter, smooth an image by preserving the edges. It can be applied using fslmaths:
fslmaths <input_image> -fmedian <output_image>
It happens that an image has not a homogeneous intensity field. In MRI, the intensity is proportional to the antena proximity.
N3 - Non-parametric Non-uniform Intensity Normalization#
Information can be found on http://en.wikibooks.org/wiki/MINC/Tools/N3
This filter can be applied using the following command (MNI tools): (Problem –> lost the image intensity dynamic)
mri_nu_correct.mni --i <input_image> --o <output_image>
Or with c3d:
c3d <input_image> -biascorr -o <output_image>
The N4 algorithm is a variation of the original N3 algorithm with the additional benefits of an improved B-spline fitting routine which allows for multiple resolutions to be used during the correction process.
This algorithm is implemented on ITK (http://www.itk.org/Doxygen/html/classitk_1_1N4BiasFieldCorrectionImageFilter.html)
or in c3d:
c3d <input_image> -n4 -o <output_image>
Example (before-after N4 correction):