214 Works

Peaks extraction

Giulia Berto
App to extract the peaks of a spherical harmonic function at each voxel.

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).

HCP Pipeline (PostFreeSurfer)

Kate Alpert
BIDS app for HCP post-FreeSurfer for BrainLife. Outputs include surface topologies and features resampled onto the high (164k) dimensional atlas space as well as myelin mappings. (Please see https://github.com/Washington-University/HCPpipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#structural-preprocessing for more information on HCP structural pipelines.)

Fit CSA

Soichi Hayashi, Serge Koudoro & Aman Arya
Fits a CSA model to diffusion data (dipy_fit_csa)

HCP Pipeline (PreFreeSurfer)

Soichi Hayashi & Kate Alpert
BIDS app for HCP pre-FreeSurfer for BrainLife. Performs ACPC alignment, FNIRT-based brain extraction, and bias field correction. (Please see https://github.com/Washington-University/HCPpipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#structural-preprocessing for more information on HCP structural pipelines.)

Network Neuro

Soichi Hayashi, Paolo Avesani, Franco Pestilli & Brent McPherson
Build structural brain networks using diffusion-weighted MRI, tractography and a brain atlas for cortical and subcortical parcellation.

Ensemble Tracking with dtiInit

Lindsey Kitchell, Franco Pestilli, Brent McPherson & 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...

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.

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...

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.

DP Profile with DWI

Soichi Hayashi & Cesar F. Caiafa
Generate FA profiles

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.

Track between multiple brain regions from atlas

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

Crop and Reorient T1

Soichi Hayashi & Lindsey Kitchell
This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.

Posterior Associative White Matter Tracts Segmentation

Franco Pestilli & Daniel Bullock
This brainlife.io App implements the white matter segmentation of the vertical tracts described in Bullock et al. 2019. It segments 8 (4 per hemisphere) white matter tracts, the posterior Arcuate (pArc), temporal-parietal connection (TPC), middle-longitudinal fasciculus (MdLF-SPL MdLF-Ang) and the vertical occipital fasciculus (VOF).

multi-LAP with trk

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

app-repeat-tracking

Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

LiFE with dtiInit

Soichi Hayashi, Paolo Avesani, Lindsey Kitchell & Franco Pestilli
LiFE (Linear Fasicle Evaluation) predicts the measured diffusion signal using the orientation of the fascicles present in a connectome. LiFE uses the difference between the measured and predicted diffusion signals to measure prediction error. The connectome model prediction error is used to compute two metrics to evaluate the evidence supporting properties of the connectome.

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.

FSL BET Brain Extraction (DWI)

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

BIDS Tracula

Kate Alpert
BIDS app for FS Tracula for BrainLife

Registration Year

  • 2018
    140
  • 2019
    74

Resource Types

  • Software
    214