224 Works

Convert trk to tck in T1 space

Soichi Hayashi & Paolo Avesani
Convert a tractogram in tck format to a trk format file in T1 space

DWI preproc and nonlinear registration to T1

Kate Alpert
App for running mrtrix3 dwipreproc and then performing nonlinear registration of dwi to T1 (by running ANTs affine+nonlinear registration of CSF masks of mean b0 and T1). Bvectors are rotated with the affine transform. App is recommended for bringing dwi to T1 space if no phase encoding contrast between b=0 images was collected (so mrtrix3 dwipreproc cannot perform inhomogeneity field estimation).

Split Shells

Soichi Hayashi & Lindsey Kitchell
Split multi-shell diffusion data into a single chosen b value shell while rounding bvals

HRSC: High Resolution Structural Connectome Processing

Kate Alpert
App for running high resolution structural connectome processing from Pierre Besson


Soichi Hayashi & Serge Koudoro
Reslice a dMRI dataset to have isotropic voxel size (dipy_reslice)

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.

ROI Trekker

Soichi Hayashi, Franco Pestilli, Dogu Baran Aydogan, Brent McPherson & Brad Caron


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

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.)


Soichi Hayashi, Sofie Van Den Bossche, Madhur Tandon, Guorong Wu, Franco Pestilli & Daniele Marinazzo
Hemodynamic Response Function Retrieval and Deconvolution (RS-HRF)

AFQ Tract Classification with LiFE

Soichi Hayashi, Lindsey Kitchell & Franco Pestilli
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...

The major white matter tracts tissue microstructure predict collison-sport participation

Franco Pestilli & Brad Caron
We present processed data from an investigation of the effects of long-term exposure to repetitive head impacts and brain tissue microstructure. Participants included 4th and 5th year varsity IU football players, 4th and 5th year varsity IU cross-country runners, and senior non-athlete IU students. We publish this dataset in hopes TBI researchers will be able to reproduce our results and perform new analyses to accelerate understanding.


Brent McPherson
repeat of fixed parameters for OHBM 2019 submission


Aditya Gupta
This is an application I am developing for the Franco Pestilli's Brainlife Platform.

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).

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

Prepare PRF output for visualization

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


Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

multi-LAP and multi-NN (deprecated)

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

FSL BET Brain Extraction (DWI)

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

Registration Year

  • 2018
  • 2019

Resource Types

  • Software