140 Works

Compute SNR on Corpus Callosum

David Hunt
Brainlife.io app that computes the signal-to-noise ratio in the corpus callosum

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.


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.

Plot tract measures

Giulia Berto
Compute and plot total number of fibers, total number of nodes and average length of some tracts.

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.

Convert wmc to multiple trk

Soichi Hayashi & Paolo Avesani
Takes a white matter classification resulting from a tract segmentation app and outputs one trk file for each segmented tract.

Multi-Atlas Transfer Tool

Soichi Hayashi, Josh Faskowitz, Franco Pestilli, Brent McPherson & Brad Caron
brainlife.io version of multi atlas transfer tools (maTT). Specifically, this is an implemenation of maTT2, which uses the gcs files trained on the mindboggle-101 data. The GCS files are automatically pulled from the maTT fishare directory if not present locally. Inputs include: freesurfer, t1, atlas. Outputs include: parc.nii.gz (for each atlas indicated) & remapped LUT text file (for each atlas indicated). These outputs are in the space of the T1w that was submitted to FreeSurfer's...

Bias Field Correction (anat/t1w)

Soichi Hayashi & Lindsey Kitchell
This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm


Soichi Hayashi, Serge Koudoro & Aman Arya
Tesor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)

White Matter Anatomy Segmentation with LiFE

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

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.)

Check dtiInit Orientation

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

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).

ROI Generation (w/ dtiinit)

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

Convert trk to tck

Soichi Hayashi
Convert trk (trackvis) file to tck (mrtrix) format

Segment tracts between multiple brain regions from ROI directory

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.

Tract Analysis Profiles

Brad Caron
This app has been deprecated. It will only work with wmc_deprecated datatype.

ROI to ROI Tracking

Ilaria Sani, Soichi Hayashi, Franco Pestilli & Brad Caron
This app will perform tracking between 2 cortical regions of interest (ROIs) from either a freesurfer parcellation or an atlas parcellation. Inputs include: parcellation (freesurfer; atlas optional) with ROI niftis (generated from app-roiGeneration), dt6 from dtiinit, and ROI pairings. Outputs include a track.tck for each pairing of ROIs, a classification structure, and a fg_classified structure which can then be fed into other apps on the website (example: Clean WMC Output).

LAP multiple examples without LiFE

Giulia Berto
This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

MRtrix2 Tracking with dtiInit

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service uses mrtrix 2.0 to track using three methods DTI-based Deterministic, CSD-based Probabilistic and Deterministic. It generates three separate tractograms (TCK), one for each algorithm.

LiFE (dwi)

Soichi Hayashi & 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.

MRtrix2 Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
This service runs mrtrix 2.0 tracking spanning over multiple tracking methods and parameters (Probabilistic and Deterministic tracking). It generates three separate tracking outputs for each algorithm.

Registration Year

  • 2018

Resource Types

  • Software