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2019_projects

Directory of Neurohackademy 2019 projects

2024-open-source-standards-report

2024-open-source-standards-workshop

The website for the workshop "An Open Source Model for Data/Metadata Standards", April 8-9, 2024

accseg

An anatomically defined, subject specific tractography segmention of connections to the human anterior cingulate cortex via dockerized processing steps.

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-createmni_rois_and_warp2subj

app-de-island_parcellation

Remove islands (unconnected components) from and/or inflate a given volumetric parcellation.

app-dipy-connectome_and_wmc_from_parc

Generate a structural connectivity matrix and a White Matter Classification structure for a given parcellation and tractogram.

app-dipy-workflows

Brainlife wrapper app for Dipy workflows.

app-filterviaquickbundles

app-generatetractmasks

app to generate binary masks of the segmented fiber tracts

app-hcp-pipeline

brainlife wrapper for HCP Pipelines

app-life_afq_qualitycheck

Generates multiple graphs that can be used as a quality check for the outputs of AFQ and LiFE. This application will only work if the zero weighted fibers are removed AFTER AFQ.

app-mrtrix3-act

Runs mrtrix3 ACT (Anatomically Constrained Tractography) using either single- or multi-shell diffusion-weighted MRI data.

app-nhp_hcp_preproc

app-probtrackx_connectome

app-probtrackx_connectome-nipype

app-qsiprep

Preprocessing of diffusion MRI data.

app-segment_with_rois

app-snr_report

app-tcks_to_tck_and_wmc

Simple converter for the multi-tck format, tcks, which combines these into a single tck file and produces an associated WMC file.

app-template-python

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

app-track_alic

Containerized app for tracking the anterior limb of the internal capsule (in humans)

app-tractclassification

Classify major human white matter tracts

app-voxeleronoct

This app computes the mean and standard deviation of Voxeleron OTC data for each degree of visual angle. This can be computed within a single layer, or across layers. The output of this app is a table for both mean and standard deviation, and the output data (visual angle OCT data) for each combination of eye and layer combination.

app-warp_refroi_to_subjspace

A generic template app for warping a provided ROI (situated in a reference space) to a given subject space.

app-wma_pytools-tractfigs

An app for generating multiple different kinds of figures from an input set of tracts (e.g as represented by a WMC object)

app-wmaseg

Classifies streamlines into known anatomical tracts.

atlaskit

Tools for working with brain atlas labels

atlastractsegment

2021 Bloomington hackathon working repo for prototype WM atlas tract segmentation method