215 Works

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.

Segment tractogram into fiber categories

Franco Pestilli & Daniel Bullock
Segments all streamlines from an input tractogram in to general categories (i.e. fronto-temporal, parieto-occipital etc).

wmaSeg - Giulia's patch

Giulia Berto
Classifies streamlines into known anatomical tracts.

Associative white matter connecting the dorsal and ventral posterior human cortex

Franco Pestilli & Daniel Bullock
We present cortical endpoint termination data from a series of associative white matter tracts connecting the posterior human brain cortex. These tracts include the vertical occipital fasciculus (VOF), the posterior arcuate fasciculus (pArc), the temporo-parietal connection (TP-SPL), and the middle longitudinal fasciculus (MdLF).

ROI Generation

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

DP Profile with DWI

Soichi Hayashi & Cesar F. Caiafa
Generate FA profiles

Non Local Means Denoising

Serge Koudoro
Applies nlmeans denoise (dipy / dipy_nlmeans)

Tract Analysis Profiles_deprecated

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

Registration Year

  • 2018
    139
  • 2019
    76

Resource Types

  • Software
    215

Data Centers

  • Brainlife Production
    215