Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.
Classifies streamlines into known anatomical tracts.
Fit MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng. Either the laplacian or positivity or both must be set to True. (dipy_fit_mapmri)
Brain Extraction via FSL's BET command
Will take a dt6 and create tensor (FA,MD,AD,RD) and Westin Shape Indices (cl, cp, cs) nifti images from a dt6.mat structure.
Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1
Tensor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)
Provides useful information about different files used in medical imaging.
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters
This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.
This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs) and an optional brainmask of the DWI. Will output the four NODDI output files: neurite density index (ndi), orientation dispersion index (odi), isotropic volume fraction (isovf), and the directions (dirs).
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.
Code to convert wmc to trk and resample with the given step size.
This app segments tracts using pairs of (potentially multiple) specified rois from an roi directory to output a set of tracts.
Convert a white matter classification (wmc) structure to a tractogram as a single trk file
Convert a tractogram in tck format to a trk format file in T1 space
This App creates a large set of candidate streamlines using an ensemble of algorithms and parameter values. All outputs will be then combined into a single track.tck output.
Application to calculate the Laplace Beltrami Spectrum and Eigenvectors using Matlab.
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.
This app uses the Automatic Registration Toolbox (ART) to perform ACPC alignment of the T1 image. See https://www.nitrc.org/projects/art/ for more information.
This application will provide a recommendation on which axis you should flip the bvecs of your data, if it is necessary. It will perform fiber tracking using 4 different gradient flip options (no flip, x flip, y flip, and z flip) and report the most likely flip needed for your data. The flip recommendation is made based on the flip direction with the highest number of long fibers.