207 Works

Resample tck

Giulia Berto
Code to resample a tck file with a given step size.

Track between multiple brain regions from atlas

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

Binary Tract Masks

Soichi Hayashi & Lindsey Kitchell
app to generate binary masks of the segmented fiber tracts

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).

HCP Pipeline (FreeSurfer)

Kate Alpert
BIDS app for HCP FreeSurfer for BrainLife. Requires T1w_acpc_dc_restore.nii.gz, T1w_acpc_dc_restore_brain.nii.gz, and T2w_acpc_dc_restore.nii.gz from PreFS pipeline. (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.)

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.

Crop and Reorient T2

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

HRSC: High Resolution Structural Connectome Processing

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

CSA Peaks

Aman Arya
This service generates a csa model using dipy from a given dwi file and freesurfer mask. It then saves the evaluated peaks of the csa model into a dipy compatible .pam5 (peaks and models 5) file type for use in other dipy applications and scripts.

Bias Field Correction (anat/t1w)

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

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...

Convert wmc to trk

Paolo Avesani
Convert a white matter classification (wmc) structure to a tractogram as a single trk file

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.

Convert brainmask from dtiinit

Brad Caron
temp app to convert brainmask from dtiinit to mask datatype

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...

Shape Signature

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.

Round b-values / Flip b-vecs for dtiInit

Soichi Hayashi & Lindsey Kitchell
Deprecated - use split shell directly.

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.

Convert trk to tck

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

Diffusion Predictor Grid Search (AppA) (old)

Soichi Hayashi
This is an old version that used dwi instead of dtiinit


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

FSL BET Brain Extraction

Soichi Hayashi & Lindsey Kitchell
Brain Extraction via FSL's BET command

Anatomically-informed multi-LAP

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

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...

Registration Year

  • 2018
  • 2019

Resource Types

  • Software

Data Centers

  • Brainlife Production