144 Works

Convert tractmeasures datatype to tractprofile datatype

Brad Caron
undefined

Benchmark Bundle Segmentation

Giulia Berto
Dataset for human white matter bundles segmentation methods benchmark. The dataset contains 72 bundles per subject, segmented with a semi-automatic procedure described in [Wasserthal et al. 2018].

Extract shell from DWI image

Brad Caron & Sophia Vinci-Booher
This app will extract diffusion gradient (i.e. shell) volumes from a DWI image using MrTrix3’s dwiextract function. Based on user input, will either include or exclude bzero volumes.

Trekker - scalar testing

Soichi Hayashi, Franco Pestilli, , Brent McPherson & Brad Caron
Brainlife App (wrapper) for dMRI based fiber tracking using parallel transport tractography https://dmritrekker.github.io

Generate ROIs for Visual White Matter Tracking in dMRI Space (Glasser Parcellation) Binned by prf Eccentricity Estimates

Brad Caron
This app will generate ROIs that can be used for visual white matter tracking, including optic radiation tracking. This includes visual areas from the Glasser parcellation, the left and right LGNs from a thalamic nuclei segmentation, and exclusion ROIs from freesurfer. The ROIs will be resliced into diffusion space in of this. The Glasser ROIs will be binned by Eccentricity based on pRF mapping

EFC identifiability

App on processing, analyzing eFC

Network Plot Degree Distribution

Example template for network template using matlab

Remove first volumes of fMRI

Amin Saberi
Simple Brainlife app which removes the first volumes of fMRI images

FSL Reorient - Task

Soichi Hayashi, Brent McPherson & Brad Caron
Uses fslreorient2std to reorient an image in standard orientation.

Test bl2bids conversion

Giulia Berto
Application for Big Computational Data Specification (v1.1). This specification provide information on how to write an Application that can run on the open platform

MAIA microperimetry analysis

Daniel Bullock & Soichi Hayashi
A brainlife.io app for computing the degree-based ring averages for microperimetry measurements

Edge time series

Farnaz Zamani Esfahlani
undefined

Clean parcellations

Brad Caron
undefined

Reslice ROIs to match input anatomy

Brad Caron
undefined

FSL Eddy-correct

Brad Caron
This app will run eddy_correct on a diffusion-weighted MRI (DWI) image. This app is intended to be used on datasets that have either 1) have already been corrected via top-up or 2) cannot be corrected with top-up. This will

Resample cortexmap data to a standard mesh using Connectome Workbench

Brad Caron
This app will take surf and func data from cortexmap datatype and resample to a standard mesh. This will be useful for performing group averaging of surface maps.

app-test

Aurore Bussalb
This a little App to test registration steps on Brainlife and to test how to run it.

MNE-BIDS-Pipeline: [1] MEEG preprocessing

Julia Guiomar Niso Galan
This Brainlife App imports and preprocess MEG (and EEG) files using MNE-BIDS-Pipeline (https://mne.tools/mne-bids-pipeline).

Map tract endpoint ROIs to cortical surface for quantitative analyses

Brad Caron
This app will map volumated measure files (i.e. tensor, NODDI) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.

Cortex Tissue Mapping (Native & Template Space) - Myelin Mapping (T1w/T2w ratio) (No SNR masking)

Brad Caron
This app will map volumated measure files (i.e. tensor, NODDI) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.

Cortex Tissue Mapping (Native Space) - Myelin Mapping (T1w/T2w ratio) (No SNR masking)

Brad Caron
This app will map volumated measure files (i.e. tensor, NODDI) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.

app-skullStrip

Eva Bacas
brainlife app - runs AFNI's skullstrip function on NIfTI files

Extract DWI volumes of choice

Brad Caron
This app will extract volumes of interest from DWI data

Generate ROIs in Anatomical Space

Brad Caron
This app will generate ROIs from a parcellation, subcortical structures found in the Freesurfer aseg, cortical structures found in the Freesurfer parcellations, and population receptive field visual area segmentations. The ROIs will be resliced into anatomical space. Merging of rois is allowed.

MNE - Autoreject

Julia Guiomar Niso Galan
MNE Artifact Rejection based on Autoreject https://autoreject.github.io [1] Mainak Jas, Denis Engemann, Federico Raimondo, Yousra Bekhti, and Alexandre Gramfort, "Automated rejection and repair of bad trials in MEG/EEG." In 6th International Workshop on Pattern Recognition in Neuroimaging (PRNI), 2016. [2] Mainak Jas, Denis Engemann, Yousra Bekhti, Federico Raimondo, and Alexandre Gramfort. 2017. "Autoreject: Automated artifact rejection for MEG and EEG data". NeuroImage, 159, 417-429.

Registration Year

  • 2021
    144

Resource Types

  • Software
    144