This app will generate images (jpgs) of data mapped to the cortical surface using MNE-python's (https://mne.tools/stable/index.html) build of pysurfer (https://pysurfer.github.io/index.html).

App on processing, analyzing eFC

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Simple brainlife app to create a network from a conmat matrix.

This is the official C-PAC (Configurable Pipeline for the Analysis of Connectomes) brainlife.io app. Currently this app runs either the default pipeline or one of our preconfigured pipelines.

This app will generate ROIs that can be used for visual white matter tracking, including optic radiation tracking. This includes V1 from a pRF visual area segmentation, 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.

This app uses [Trekker](https://dmritrekker.github.io) to Track the Human Optic Radiation.

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Filtering out of artifactual streamlines from a tractogram with a geometric deep learning model

Runs FitFullModelSampleAllTracts to find the optimal parameters and fit model with the optimal parameters.

Classifies streamlines into known anatomical tracts.

Fit MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng. Either the laplacian or positivity or both must be set to True. (dipy_fit_mapmri)

Will take a dt6 and create tensor (FA,MD,AD,RD) and Westin Shape Indices (cl, cp, cs) nifti images from a dt6.mat structure.

Runs vistasoft/dtiInit to preprocess and register dwi to anat/t1

Tensor reconstruction and compute DTI metrics using weighted least-squares (dipy_fit_dti)

Provides useful information about different files used in medical imaging.

Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

This application will create a mask nifti file of the white matter of the T1 image using Freesurfer's aparc+aseg.mgz parcellation.

This app will fit the Neurite Orientation Dispersion and Density Imaging (NODDI; Zhang et al, 2012) model to multi-shell, normalized DWI data using the Accelerated Microstructure Imaging via Convex Optimization (AMICO; Daducci et al, 2015) toolbox. Requires normalized, multi-shell DWI data (including bvals and bvecs) and an optional brainmask of the DWI. Will output the four NODDI output files: neurite density index (ndi), orientation dispersion index (odi), isotropic volume fraction (isovf), and the directions (dirs).

This app performs automatic example-based tract segmentation using the Linear Assignment Problem (LAP) algorithm having multiple examples.

Code to convert wmc to trk and resample with the given step size.

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Brainlife App (wrapper) for dMRI based fiber tracking between ROIs using parallel transport tractography

Datasets and derivatives generated for Brad Caron's Qualifying exams.