Brain Life

United States of America

93 Works

Tract Profile Aggregator

Soichi Hayashi
Tract Profile Output Aggregator

Network Neuro Aggregator

Soichi Hayashi
Network Neuro Output Aggregator

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.

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.

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.

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.

Volume-based Multiple Linear Regression

Soichi Hayashi
SOCR KW wrapper for Brainlife

SOCR Volume-based Multiple Linear Regression

Soichi Hayashi
SOCR KW wrapper for Brainlife

HCP Pipeline

Soichi Hayashi
Run HCP Pipeline powered by BIDS app

DP Remove Tracts

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

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.)

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.)

HCP Pipeline (PreFreeSurfer)

Soichi Hayashi & Kate Alpert
BIDS app for HCP pre-FreeSurfer for BrainLife. Performs ACPC alignment, FNIRT-based brain extraction, and bias field correction. (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.)

BIDS Mrtrix3 Connectome

Kate Alpert
BIDS app for Mrtrix3 Connectome DTI processing for BrainLife

BIDS Tracula

Kate Alpert
BIDS app for FS Tracula for BrainLife

Mouse Segmentation Pipeline

Soichi Hayashi, Lei Wang & Kate Alpert
Pipeline for mouse brain skull-stripping and ROI segmentation

Brain reconstruction

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

Recobundles

Serge Koudoro & Aman Arya
This application takes in a full tractography (Multishell Tractography w/CSA or Multishell Tractography w/ SHORE) and the output from the White Matter Segmentation and uses the Recobundles algorithm to find the corresponding white matter segmentation in the full tractogram.

Non Local Means Denoising

Serge Koudoro
Applies nlmeans denoise (dipy / dipy_nlmeans)

Clever

Steven O'Riley & Soichi Hayashi
Clever

Segmentation with Median Otsu

Soichi Hayashi & Serge Koudoro
Brain segmentation with the median_otsu method using DIPY. Default parameters work well on most volumes but you can play with them if needed

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.

mrtrix3 preprocess

Brent McPherson
run the recommended preprocessing procedure provided by mrtrix3.

MAPMRI Fitting

Soichi Hayashi, Serge Koudoro & Aman Arya
Fit MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng. Either the laplacian or positivity or both must be set to True. (dipy_fit_mapmri)

Deterministic Tracking

Soichi Hayashi & Aman Arya
Deterministic tracking using a peaks and metrics (PAM) (dipy_track_det)

Resource Types

  • Software
    93

Publication Year

  • 2018
    59
  • 2017
    34

Registration Year

  • 2018
    93

Data Centers

  • Brainlife Production
    93