138 Works

Trekker ROI Tracking

Brad Caron, & Soichi Hayashi
Brainlife App (wrapper) for dMRI based fiber tracking between ROIs using parallel transport tractography

Brad Quals

Brad Caron
Datasets and derivatives generated for Brad Caron's Qualifying exams.

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).


Giulia Berto
Code of Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation.

Remove Tract Outliers (new wmc input/output) - copy

Daniel Bullock

Generate tract endpoint maps

Daniel Bullock
This app will generate endpoint maps for all tracts in an input classification structure. User can specify what sort of decay/smoothing algorithm can be used (or none).

Life reorient test

David Hunt

Shape Signature

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
This App takes tract masks and convert them to series of numerical values that chracaterizes each masks. The numerical values are generated from the flattened output of 3D convolutional layers of the model trained to classify tract names. Output values could be used as a "shape signature" and compared against other similar shaped tracts.

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.

WMC Figures (AFQ or WMA)

Brad Caron & Lindsey Kitchell
This service creates 4 figures of each AFQ tract: axial, left sagittal, right sagittal, coronal. Please choose the t1 image slices you would like displayed. The default slices work well for the HCP t1 images if they have not been re-ACPC aligned. If you have ACPC aligned your t1 images using the ACPC alignment app on Brain Life the following values are a good starting point: coronal = 105, sagittal = 89, axial = 65....

old ensemble tracking

Lindsey Kitchell & 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.


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


Soichi Hayashi
To monitor app-stage

Remove Tract Outliers

Daniel Bullock

wmaSeg - Giulia's patch

Giulia Berto
Classifies streamlines into known anatomical tracts.


Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

multi-LAP and multi-NN with trk

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

DSC evaluation (mask - mask)

Giulia Berto
Compute the degree of overlap between two bundle masks using the Dice Similarity Coefficient (DSC) score.

Generate ROIs from an atlas

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

Fit Constrained Deconvolution Model for Tracking

Brad Caron & Brent McPherson
This will fit the constrained spherical deconvolution model to an input DWI image. The outputs from this can be used for subsequent tracking apps.

NODDI Amico (single shell) - Deprecated

Brad Caron
This fits the NODDI model on single shell data. The only value that should be trusted is orientation dispersion (OD), as this measure can be fit accurately with single shell data


Robert Puzniak
Improved version of the mrtrix3-preproc script deployed on BrainLife platform

Freesurfer on OSG

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Submit Freesurfer workflow on Open Science Grid (A national, distributed computing partnership for data-intensive research)

Convert wmc to trk

Soichi Hayashi
Convert a white matter classification (wmc) structure to a tractogram as a single trk file. Segmentation ID will be used to set bundle_code inside the .trk. You can access it with trk.tractogram.data_per_streamline[0]["bundle_code"] with nibabel



Registration Year

  • 2019

Resource Types

  • Software