abcd-spec

Brain Data Application Specification

acnn-website

Website for ACNN

actigraphy-app

This is a template for a python-based brainlife.io/app

afq

Automated Fiber Quantification

al-folio

A beautiful, simple, clean, and responsive Jekyll theme for academics

amd

Diffusion MRI in AMD patients

app-3dfreesurfs

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

app-3dpialwm_freesurfer

This application converts Freesurfer's pial and white matter surfaces to different file types. It will convert the lh/rh.pial, lh/rh.white, lh/rh.smoothwm, lh/rh.inflated files into your choice of file type (stl, vtk, gii, mgz)

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-align_hcp_to_native_space

Aligns HCP fMRI data in MNI space to subject space

app-analyzeprf

app-benson14-retinotopy

Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

app-biasfieldcorrection

This application will correct for bias field issues in T1 images using ANTs N4BiasFieldCorrection algorithm

app-binvolvolume

computes the volume of binary nifti images

app-classifiedfibertractstats

This will give you the fiber count, mean length, standard deviation of length, total length, and volume of each fiber tract classified by AFQ or WMA.

app-connectivity-gradient

Compute connectivity gradients using functional MRI data

app-converttck2trk

This service will convert mrtrix tck files to tractvis trk files

app-decimatemesh

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

app-generatetractsurfaces

app to generate surfaces of each fiber tract

app-helloworld

Brainlife.io tutorial App

app-lbspectrum_matlab

Application to calculate the Laplace Beltrami Spectrum and Eigenvectors using Matlab.

app-mergetck

Merge multiple TCK files into one TCK file.

app-midpreproc

app-plot3dobjects

This service creates images of 3D surfaces of the major tracts segmented by AFQ or WMA in 4 views: axial, coronal, left and right sagittal.

app-ploteigenfunctions

App to plot the eigenfunctions of the Laplace Beltrami Spectrum.

app-qwarp

runs AFNI's 3dQwarp function over a NIfTI file

app-reconstructlbeigenfunction

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

app-sift2-connectome-generation

app-steklovspectrum

app to calculate the Steklov Operator Spectrum on 3D surfaces

app-streamlinecategorysegmentation

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