Brainlife App (wrapper) for dMRI based fiber tracking using parallel transport tractography https://dmritrekker.github.io

Test

Example template for network template using matlab

App on processing, analyzing eFC

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

test

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.

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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.

brainlife.io version of multi atlas transfer tools (maTT). Specifically, this is an implementation of maTT2, which uses the gcs files trained on the mindboggle-101 data. Outputs include: parc.nii.gz (for each atlas indicated) & remapped LUT text file (for each atlas indicated). Please consult the output parcellation key for the names of the nodes produced. These outputs are in the space of the T1w that was submitted to FreeSurfer's recon-all processes. In other words, the parc.nii.gz...

This app will convert important parcellation statistics, including volume of each individual ROI given in a parcellation. These can be used for group analyses. This app should be used whenever possible to compute parcellation statistics (uses freesurfer's mri_annotation_stats).

brainlife wrapper for HCP Pipelines

Apply MaxFilter on MEG signals using MNE Python.

This app will This app will compute multiple summary statistics from measures mapped to the cortical midthickness surface on a per-ROI basis. This app takes in a cortexmap datatype and an optional parcellation/surface datatype. This app will compute the following summary statistics: minimum, maximum, mean, median, mode, standard deviation, sample standard deviation (n-1), and nonzero vertex count. The app will output a csv for each summary measure summarizing the diffusion measures in each ROI parcellation....

Template app to build new network neuroscience apps for brainlife

prueba

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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.

Example template for network template using matlab

Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA

Example template for network analyses using matlab inside brainlife.

A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning