Image correction software tools | Magnetic resonance imaging analysis
Intensity non-uniformity correction is required because MR images are known to contain low frequency spatial intensity variations often referred to as radio frequency inhomogeneity or shading artifact. All segmentation algorithms in brain MRI must account for this artifact to produce accurate segmentations.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
Deletes non-brain tissue from an image of the whole head. BET can also estimate the inner and outer skull surfaces, and outer scalp surface, if T1 and T2 input images are of good quality. It is very robust and accurate and has been tested on thousands of data sets from a wide variety of scanners and taken with a wide variety of magnetic resonance sequences. BET uses a deformable model that evolves to fit the brain's surface by the application of a set of locally adaptive model forces. The method is very fast and requires no preregistration or other pre-processing before being applied. BET takes about 5-20 sec to run on a modern desktop computer and is freely available, as a standalone program that can be run from the command line or from a simple GUI, as part of FSL (FMRIB Software Library).
Increases the local contrast of an image. CLAHE uses the contrast limited adaptive histogram equalization to process. The contrast amplification in the vicinity of a given pixel value is delivered by the slope of the transformation function. This ImageJ plugin has three main parameters: block size, histogram and max slope.
Converts coordinates between the Montreal Neurological Institute (MNI) and Talairach spaces. Icbm2tal facilitates the insertion into a database. This coordinate-based tool transformation accomodates spatial disparity and is also available within GingerALE or can be downloaded as MATLAB files.
Serves for iterative image deblurring. PID allows users to deconvolve a color image by splitting the channels and deblur each channel separately. It contains a graphical user interface (GUI) permitting users to specify several types of details such as stopping tolerance, threshold, or log convergence.
Adjusts intensity non-uniformity in 3D magnetic resonance (MR) images. N3 models non-uniformity as a smooth multiplicative field to obtain an approximation of the tissue dependent character of excitation field non-uniformity. It allows violations of the stationarity assumption and considers that the image intensities are independent identically distributed random variables. It uses also and iterative method to assess the distribution of the true tissue intensities and the multiplicative bias field.
Processes the diffusion of magnetic resonance imaging (MRI) data. TORTOISE contains three main modules: DIFF_PREP-software for image resampling, motion, eddy current distortion, and EPI distortion correction using a structural image as target, and for re-orientation of data to a common space; DIFF_CALC-software for tensor fitting, error analysis, directionally encoded color map visualization and ROI analysis; DR-BUDDI-software for EPI distortion correction using pairs of diffusion data sets acquired with opposite phase encoding (blip-up blip-down acquisitions).