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).
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.
Assists users in electron paramagnetic resonance (EPR) data acquisition derived from EMX spectrometers. WinEPR includes a monitoring system intending to ease bridge tuning, resonator calibration, and experiment execution as well as automated processes. This program supports both CW-EPR and CW-ENDOR spectra. Features provided by this software had been integrated into the Xenon application.
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.
Offers a set of methods for computational anatomy. CAT extends segmentation methods supplied by the SPM software by furnishing two approaches to reduce noise, an internal interpolation as well as multiple techniques encompassing local adaptive segmentation (LAS). The application enables application in: (i) voxel-based morphometry (VBM); (ii) deformation-based morphometry (DBM); (iii) region- or label-based morphometry (RBM) as well as (iv) surface-based morphometry (SBM).
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.