236 Works

EPI T1 Registration

Soichi Hayashi & Brad Caron
This app will register DWI images to a T1 image, fit a tensor model, and create a dt6.mat file using FSL. Inputs are normalized DWI data and a T1 image. Main outputs are a dt6.mat file, a dt6.json file, and dwi_aligned_trilin files (aligned DW data, bvecs, bvals).

rsHRF

Soichi Hayashi, Sofie Van Den Bossche, Madhur Tandon, Guorong Wu, Franco Pestilli & Daniele Marinazzo
Hemodynamic Response Function Retrieval and Deconvolution (RS-HRF)

White Matter Anatomy Segmentation

Daniel Bullock
Classifies streamlines into known anatomical tracts.

Tractography quality check (trk)

Daniel Bullock
A quality check application for tractography, segmentatations, and LiFE structures. For the whole brain tractogram, provides a number of statistics associated with average streamline characteristics (i.e. count, volume occupied, avg length, length distribution). Does the same for the positively weighted streamlines of an FE structure if input. If a classification structure is input, provides a number of macrostructural statistics like stream count, volume, avg length, whole brain count/volume proportion, etc).

TractSeg

Soichi Hayashi, Lindsey Kitchell & Jakob Wasserthal
Brainlife App for MIC-DKFZ/TractSeg. A tool for fast and accurate white matter bundle segmentation from Diffusion MRI using pretrained pytorch ML model.

Laplace Beltrami Spectrum: Eigenvalues Only

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum using matlab

Convert tck+dwi to trk (MRtrix 2)

Soichi Hayashi & Lindsey Kitchell
Converts a tck that was made using MRtrix 2 into a trk in the dwi space.

mergeTCK

Sophia Vinci-Booher
Merge multiple TCK files into one TCK file.

Tensor Mask

Soichi Hayashi, Serge Koudoro & Aman Arya
generate a mask from FA

TractSeg test

Pietro Astolfi, Paolo Avesani & Giulia Berto
Automatic White Matter Bundle Segmentation

DP Fit Model with DWI

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

Decimate 3D surfaces

Lindsey Kitchell
This application will reduce the number of vertices and faces on 3D surfaces by the percent reduction chosen.

dtiInit

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

Check T1 Orientation

Soichi Hayashi & Lindsey Kitchell
This application checks and reports the orientation (neurological or radiological) of a nifti file.

Associative white matter connecting the dorsal and ventral posterior human cortex

Franco Pestilli & Daniel Bullock
We present cortical endpoint termination data from a series of associative white matter tracts connecting the posterior human brain cortex. These tracts include the vertical occipital fasciculus (VOF), the posterior arcuate fasciculus (pArc), the temporo-parietal connection (TP-SPL), and the middle longitudinal fasciculus (MdLF).

TractSeg training

Pietro Astolfi, Paolo Avesani & Giulia Berto
Automatic White Matter Bundle Segmentation

DP Remove Tracts with DWI

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

ROC curve

Soichi Hayashi & Giulia Berto
Plot ROC-AUC curve for multi-LAp and multi-NN

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

clever

Steven O'Riley, Soichi Hayashi & Damon Pham
clever computes principal Components LEVERage (CLEVER) and robust distance, measures of outlyingness for high-dimensional data such as fMRI data.

Segment tracts between multiple brain regions from ROI directory (new wmc output)

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.

Registration Year

  • 2018
    140
  • 2019
    96

Resource Types

  • Software
    236