207 Works

TractSeg HCP (test)

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

Deterministic Tracking

Soichi Hayashi, Serge Koudoro & Aman Arya
Deterministic tracking using a peaks and metrics (PAM) (dipy_track_det)

Generate Equivolumetric Surfaces

David Hunt
Computes n equally spaced offset surfaces between the white and pial surfaces with equal ratios between areas of successive surfaces, which samples the same layers in gyri and sulci.

Track between multiple brain regions from atlas (new wmc output)

Franco Pestilli & Daniel Bullock
This app tracks between specified atlas regions to output a set of tracts.

White Matter Anatomy Segmentation with LiFE

Lindsey Kitchell & Daniel Bullock
Classifies streamlines into known anatomical tracts.

old ensemble tracking

Lindsey Kitchell & Brad Caron
This service uses MRtrix 0.2.12 to do ensemble tracking using tensor and constrained spherical deconvolution (csd) algorithms. It generates a large set of candidate streamlines using a tensor-based deterministic model, csd-based deterministic model, and csd-based probabilistic model. The csd-based models can be computed at lmax values of 2, 4, 6, 8, 10, and 12. All candidate streamlines are combined into a single track.mat file. If you know the max lmax value for your data input...

ANTs transformation and wmc registration with T1

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

Generate ROIs from an atlas

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

LAP single example with LiFE

Giulia Berto & Brad Caron
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm with a single example. The user can specify up to eight tracts of interest, otherwise all the tracts of the given segmentation are considered as input.

noop

Soichi Hayashi
Service that does nothing (exist to do inter-resource transfer)

Segment tracts between multiple brain regions from atlas

Franco Pestilli & Daniel Bullock
This app segments tracts using pairs of (potentially multiple) specified atlas regions to output a set of tracts.

Fit DKI

Soichi Hayashi, Serge Koudoro & Franco Pestilli
Fit a Diffusion Kurtosis Imaging model to multishell Diffusion-weighted data (dipy_fit_dki)

dev-ensembletracking

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

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

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

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.

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.

TractSeg (deprecated)

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.

Steklov Operator Spectrum

Lindsey Kitchell
app to calculate the Steklov Operator Spectrum on 3D surfaces

Quantitative Statistics of Classified Fiber Tracts

Soichi Hayashi, Lindsey Kitchell & Daniel Bullock
This will give you the fiber count, mean length, standard deviation of length, total length, and volume of each fiber tract classified by AFQ or WMA.

Laplace Beltrami Spectrum: Eigenvalues Only

Lindsey Kitchell
Application to calculate the Laplace Beltrami Spectrum using matlab

DSC evaluation

Giulia Berto
Compute the Dice Similarity Coefficient (DSC) between corresponding tracts of the given segmentation and the ground truth. The user can specify up to eight tracts of interest, otherwise all the tracts of the given estimated segmentation are considered as input.

Registration Year

  • 2018
    140
  • 2019
    67

Resource Types

  • Software
    207

Data Centers

  • Brainlife Production
    207