Pinned Repositories
3os.org
Source Code for 3os.org website. The website based on Markdown format, rendered to html and hosted on github-pages
AFQ
Automated Fiber Quantification
app-acpcART
This app uses the Automatic Registration Toolbox (ART) to perform ACPC alignment of the T1 image. See https://www.nitrc.org/projects/art/ for more information.
app-add-to-t1
This is a test app that will add a value of 1 to each voxel of a t1, and output a new t1
app-AFQ_figures
This service creates 4 figures of each AFQ tract: axial, left sagittal, right sagittal, coronal. Please choose the t1 image slices you would like displayed. The default slices work well for the HCP t1 images if they have not been re-ACPC aligned. If you have ACPC aligned your t1 images using the ACPC alignment app on Brain Life the following values are a good starting point: coronal = 105, sagittal = 89, axial = 65. The img_min and img_max values refer to the value range displayed for the t1 image. The value range is calulated as follow (mean + img_min * std, mean + img_max * std). The default values are a good starting place, adjust them if your t1 is too dark or too light.
app-AFQclean
This service cleans the output from AFQ and WMA using AFQ's AFQ_removeFiberOutliers function. For more information on the inputs of this application, please read the documentation at the top of the function: https://github.com/yeatmanlab/AFQ/blob/master/functions/AFQ_removeFiberOutliers.m
app-analyzePRF
FDS-CourseOne-Extra-Laterality
This repository is intended to be used in combination with https://github.com/psychdatascience/FDS-CourseOne. This repository contains a dataframe ('tractmeasures.csv') containing the macro- and micro-structural statistics for 61 white matter tracts across multiple data sources.
nsd-analyses
project-starter-brainlife
bacaron's Repositories
bacaron/app-compute-dsc
Compute the degree of overlap between two bundle masks using the Dice Similarity Coefficient (DSC) score.
bacaron/app-concatenate-tractmeasures
bacaron/app-convert-network-netstats
bacaron/app-dwinormalise
bacaron/app-example-shell-app
bacaron/app-fmri-2-mat
fmriprep outputs to connectivity matrices
bacaron/app-fmriprep
fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
bacaron/app-merge-tractmasks
bacaron/app-mrtrix3-act
Runs mrtrix3 ACT (Anatomically Constrained Tractography) using either single- or multi-shell diffusion-weighted MRI data.
bacaron/app-mrtrix3-preproc
Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.
bacaron/app-multiAtlasTT
brainlife.io version of maTT
bacaron/app-reslice-roi-t1
bacaron/app-visual-white-matter
bacaron/bl-conmat2network
Simple brainlife app to create a network from a conmat matrix.
bacaron/bl-metrics
bacaron/bl-network-measurements
App to calculate several basic statistics for networks and their respective null model distributions.
bacaron/brainlife
Free cloud platform for secure neuroscience data analysis.
bacaron/convert-func-nii
bacaron/dashboards
bacaron/data-science-learning
bacaron/dockerfiles
repository to store various dockerfiles used to build docker containers that are used across multiple brainlife apps
bacaron/docs
Brainlife.io Documentation
bacaron/educational-notebooks
bacaron/ga-launcher
Group Analysis container Launcher (experimental)
bacaron/HD-BET
MRI brain extraction tool
bacaron/nigerian_brain_analyses
bacaron/pybrainlife
bacaron/reorient-streamlines-ras-lpi
reorient streamlines in tck following tract profile analyses (https://brainlife.io/app/5ed02b780a8ed88a57482c92) for better RAS/LPI separation
bacaron/TractSeg
Automatic White Matter Bundle Segmentation
bacaron/validator-neuro-track
This validates a .tck file for use on brain-life