237 Works


Brent McPherson
repeat of fixed parameters for OHBM 2019 submission

Vistasoft DWI T1 Registration

Brad Caron
This app will register a DWI image to a T1w image and rotate the bvecs. Requires a DWI image (with bvals and bvecs) and an T1w image (either ACPC-aligned or native). Will output an aligned DWI image, the rotated bvecs, and the bvals files.

Tract Profiles

Soichi Hayashi & Aman Arya
This app takes in tracking data from the White Matter Segmentation app well as the nifti files of the user and gives tract profiles for each tracking file in a json format.

Crop and Reorient T1

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

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.

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.

White Matter Segmentation

Aman Arya
This service takes in a nifti and tck output from Multishell Tractography w/ CSA or SHORE and outputs the CST and ILF segmentations in .tck file format of both the left and right hemispheres.


Brent McPherson
repeat of fixed parameters for OHBM 2019 submission


Soichi Hayashi, Franco Pestilli & Brad Caron
This app will fit the diffusion tensor model (DTI) to a diffusion MRI image using FSL's dtifit commmand.


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

Check Gradient Flip

Soichi Hayashi
This app will quickly check the dwi image to see if any bvecs directions needs to be flipped. The algorithm finds bvecs that are pointing toward certain direction and find the volume slice within 4D DWI data and see how many image slices indeed seems to contain features that are orthogonal to the bvecs directions. Inconclusive output from this App usually means you have some data quality issue with your dwi.

Brain reconstruction

Soichi Hayashi & Serge Koudoro
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

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.


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

Track the Human Optic RAdiation (THORA)

Brad Caron, Dogu Baran Aydogan, Franco Pestilli & Soichi Hayashi
This app uses [Trekker](https://dmritrekker.github.io) to Track the Human Optic Radiation.

Freesurfer Group Analysis

Soichi Hayashi
Do some basic group analysis on freesurfer outputs

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.

multi-LAP and multi-NN with trk

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

mrtrix3 act sift

Brent McPherson
test of adding sift as part of streamline generation to improve segmented anatomy quality

DP Profile with DWI

Soichi Hayashi & Cesar F. Caiafa
Generate FA profiles

Registration Year

  • 2018
  • 2019

Resource Types

  • Software