215 Works

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...

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.

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.

dtiInit

Soichi Hayashi, Paolo Avesani, Lindsey Kitchell & Franco Pestilli
Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1

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).

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...

DP Remove Tracts with dtiInit

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs Gen_niftis_remove_tracts

multi-LAP with trk

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

Decimate 3D surfaces

Lindsey Kitchell
This application will reduce the number of vertices and faces on 3D surfaces by the percent reduction chosen.

Freesurfer Labels to 3D Surfaces

Lindsey Kitchell
This application will create a 3D surface for 87 freesurfer labels from the aparc+aseg.mgz file.

Resample tck

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

Crop and Reorient T2

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

Fit CSD

Soichi Hayashi, Serge Koudoro & Aman Arya
Fit a CSD model to diffusion data (dipy_fit_csd)

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.)

Reconstruct Surfaces from LB Eigenfunctions

Lindsey Kitchell
This application will reconstruct the surfaces of each 3D model based on the selected number of eigenfunctions.

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.

Plot Eigenfunctions

Lindsey Kitchell
App to plot the eigenfunctions of the Laplace Beltrami Spectrum.

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.

HCP ACPC Alignment (T2)

Soichi Hayashi, Brent McPherson & Brad Caron
This app will align a T1w image to the ACPC plane (specifically, the MNI152_T1_1mm template from FSL using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline (https://github.com/Washington-University/HCPpipelines.git). Requires a T1w image input and outputs an acpc_aligned T1w image.

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.

Split Shells

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

Noddi Amico

Brad Caron
This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs), and the single shell dwi file that has been aligned to the subject's T1 (i.e. dtiinit output) as input. The app will align the multi-shell data to the single-shell data...

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.

Registration Year

  • 2018
    139
  • 2019
    76

Resource Types

  • Software
    215