140 Works

DP Fit Model with dtiInit

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.

White Matter Anatomy Segmentation

Daniel Bullock
Classifies streamlines into known anatomical tracts.

Fit MAPMRI

Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
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)

FSL Brain Extraction (BET) on T1

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
Brain Extraction via FSL's BET command

dt6 To Nifti Converter

Soichi Hayashi & Brad Caron
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.

dtiInit

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell, Paolo Avesani & Soichi Hayashi
Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1

Fit DTI

Aman Arya, Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
Tensor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)

DWI Info

Franco Pestilli, Javier Ricardo Guaje Guerra, Serge Koudoro & Soichi Hayashi
Provides useful information about different files used in medical imaging.

Brain reconstruction

Soichi Hayashi & Serge Koudoro
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

Diffusion Predictor Grid Search (AppA)

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

White Matter Mask

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.

Noddi Amico - Deprecated

Brad Caron
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).

LAP from 5 examples

Giulia Berto
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

WMC to TRK conversion and resample

Giulia Berto
Code to convert wmc to trk and resample with the given step size.

Dtiinit Datatype Conversion

Brad Caron
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Segment tracts between multiple brain regions from ROI directory

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified rois from an roi directory to output a set of tracts.

Convert wmc to trk

Paolo Avesani
Convert a white matter classification (wmc) structure to a tractogram as a single trk file

Convert tck to trk in T1 space

Soichi Hayashi & Paolo Avesani
Convert a tractogram in tck format to a trk format file in T1 space

DP Remove Tracts with DWI

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs Gen_niftis_remove_tracts

Ensemble Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell, Brent McPherson & Brad Caron
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.

Laplace Beltrami Spectrum: Eigenvalues and Eigenvectors

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum and Eigenvectors using Matlab.

ANTs transformation and wmc registration with FA

Giulia Berto
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.

ACPC alignment via ART

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
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.

Test Gradient Flip for dtiInit processing

Brad Caron, Franco Pestilli, Giulia Berto, Lindsey Kitchell & Soichi Hayashi
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.

Test App

Soichi Hayashi
updated 3

Registration Year

  • 2018
    140

Resource Types

  • Software
    140