79 Works

TractSeg test

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

DSC evaluation (mask - mask)

Giulia Berto
Compute the Dice Similarity Coefficient (DSC) between corresponding tracts of the given segmentation and the ground truth when using HCP 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.

DSC evaluation (wmc - trk)

Giulia Berto
Compute the Dice Similarity Coefficient (DSC) between corresponding tracts of the given segmentation and the ground truth when using HCP data.

fMRI to Connectivity Matrices

Soichi Hayashi & Josh Faskowitz
fmriprep outputs to connectivity matrices

Tract Analysis Profiles

Brad Caron
Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA

TractSeg training

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

AFQ Tract Classification

Soichi Hayashi & Lindsey Kitchell
This service uses Automated fiber quantification AFQ and fe structure output from LiFE to identify major tract segments and quantify tissue properties along their trajectories. You can choose to have the zero weighted fibers (as determined by LiFE) removed before or after AFQ is applied. useinterhemisphericsplit is a variable from AFQ, which if set to true will cut fibers crossing between hemispheres with a midsaggital plane below z=-10. This is to get rid of CST...

multi-LAP with trk

Giulia Berto
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).

Decimate 3D surfaces

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

Segment tractogram into fiber categories

Franco Pestilli & Daniel Bullock
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).

wmaSeg - Giulia's patch

Giulia Berto
Classifies streamlines into known anatomical tracts.

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).

ROI Generation

Ilaria Sani & Brad Caron
This app will generate nifti files for specific ROIs, or every ROI, for a parcellation (either freesurfer or atlas).

FSL BET Brain Extraction (DWI)

Lindsey Kitchell & Brad Caron
Brain Extraction via FSL's BET command

Prepare PRF output for visualization

Soichi Hayashi
A brain life app to prepare PRF and freesurfer data to be visualized with ui-3dsurfaces

Generate ROIs from an atlas

Franco Pestilli & Daniel Bullock
Generates specified ROIS (in nifti format) from an input atlas.

dev-ensembletracking

Brent McPherson
copy of ensemble tracking that runs from the master branch for testing new changes

app-repeat-network-osg

Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

Anatomically-Informed Multiple Linear Assignment Problems for White Matter Bundle Segmentation

Paolo Avesani & Giulia Berto
A benchmark to test a tract segmentation method that takes into account information about both the underlying anatomy and the geometry of bundles at the same time.

Binary Tract Masks

Soichi Hayashi & Lindsey Kitchell
app to generate binary masks of the segmented fiber tracts

Tractography quality check (new wmc input)

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).

Registration Year

  • 2019
    79

Resource Types

  • Software
    79

Data Centers

  • Brainlife Production
    79