485 Works

pRFLife with mrTools

David Hunt
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mergeROI

Sophia Vinci-Booher
This app will merge two rois within an ROI datatype dataset into one ROI. The user must specify which two rois should be merged. The app will output one roi that contains all of the voxels that were in the two original rois.

FSL Anat (T2)

Brad Caron
This app will perform fsl_anat (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat)

Trekker ROI Tracking (DWI)

Brad Caron, , Franco Pestilli & Soichi Hayashi
This app uses [Trekker](https://dmritrekker.github.io) to track between multiple ROIs.

bold time series

Josh Faskowitz
an app to get nuisance regressed time series from a preprocessed bold, confounds, and a parc

Collegiate athlete brain data for white matter mapping and network neuroscience

Brad Caron & Franco Pestilli
We present diffusion and anatomical (T1w) processed data and derivatives from a group of IU athletes (football, cross-country) and non-athletes (students). The raw data contains both anatomical (T1 weighted) and diffusion-weighted (dMRI) magnetic resonance imaging data. The processed data shares 14 types of derivatives across 42 participants, comprising of 84 brainmasks (2 per participant), 42 Freesurfer outputs (1 per participant), 168 fiber orientation dispersion (FOD) images (4 per participant), 588 diffusion parameter maps (14 per...

Extract DWI volumes of choice

Brad Caron
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Compile tract profiles to summary structure

Brad Caron
This app will the individual tract tract profiles csv’s from the tractprofile dataype into a single summary csv for group analysis and machine learning. This app takes in a tractprofile datatype. The app will output a csv entitled ‘tracts.csv’ that can be used for group statistics and machine learning.

Track the Human Optic RAdiation - mrtrix3 iFOD2 (dtiinit)

Brad Caron
This app will generate optic radiations using MrTrix3's iFOD2 algorithm with the capability of using the Anatomically Constrained (ACT) framework

Make white matter mask in dwi space from Freesurfer (dtiinit)

Brad Caron
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dsi-studio-dwi2src

DSI Studio scripts converting DWI file to SRC format.

Little Test

Suna Guo
This is a little test of registering an app on Brainlife as part of the brain imaging course. This app takes an ACPC aligned anat/t1w data and resamples it to the desired resolution.

Test Python Template for Class

Augustin Hennings, Franco Pestilli & Tyler Larguinho
This App should be deleted. It used as an example for the class. The happy uses the code available at https://github.com/brainlife/app-template-python. The code is simple, it loads a t1w.nii.gz (which in brainlife.io is called neuro/anat) and resamples the file at the wanted resolution

Fit Constrained Deconvolution Model for Tracking

Brad Caron & Brent McPherson
This will fit the constrained spherical deconvolution model to an input DWI image. The outputs from this can be used for subsequent tracking apps.

NODDI Amico (single shell) - Deprecated

Brad Caron
This fits the NODDI model on single shell data. The only value that should be trusted is orientation dispersion (OD), as this measure can be fit accurately with single shell data

mrtrix3-preproc-impr

Robert Puzniak
Improved version of the mrtrix3-preproc script deployed on BrainLife platform

FSL Anat (T1)

Brad Caron
This app will perform fsl_anat (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat)

Freesurfer on OSG

Brad Caron, Franco Pestilli, Giulia Berto & Soichi Hayashi
Submit Freesurfer workflow on Open Science Grid (A national, distributed computing partnership for data-intensive research)

Track The Human Optic RAdiation (THORA): Contrack - Eccentricity

Brad Caron & Soichi Hayashi
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Convert wmc to trk

Soichi Hayashi
Convert a white matter classification (wmc) structure to a tractogram as a single trk file. Segmentation ID will be used to set bundle_code inside the .trk. You can access it with trk.tractogram.data_per_streamline[0]["bundle_code"] with nibabel

hello-world

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Generate ROIs in DMRI Space

Brad Caron
This app will generate ROIs from a parcellation, subcortical structures found in the Freesurfer aseg, cortical structures found in the Freesurfer parcellations, and population receptive field visual area segmentations. The ROIs will be resliced into diffusion space in of this, merging ROIs is allowed.

Segment tractogram into fiber categories

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

Network Null Model

Generates an esemble of networks according to null models that try to reproduce the data. Erdos reyni (random), Barabási-Albert and Configuration model are implemented

FSL Top-up & Eddy - CUDA

Brad Caron
This app will correct for encoding, eddy currents, and motion artifacts using FSL's Topup and Eddy functions.

Registration Year

  • 2021
    2
  • 2020
    205
  • 2019
    138
  • 2018
    140

Resource Types

  • Software
    484
  • Service
    1

Affiliations

  • The University of Texas at Austin
    4
  • Indiana University
    4