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app-ashs-segment

brainlife.io app for using Automated Segmentation of Hippocampal Subfields (ASHS) software to segment hippocampal subfields based on previously acquired atlases

app-combineroi

This app will merge two ROI datatype sets into one ROI datatype dataset.

app-denoise-tensorflow

app-freesurfer-stats

app-fsltopupeddy

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

app-hcp-acpc-alignment

This app will align a T1w image to the ACPC plane (specifically, the MNI152_T1_1mm template from FSL using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline (https://github.com/Washington-University/HCPpipelines.git). Requires a T1w image input and outputs an acpc_aligned T1w image.

app-mergedwi

Concatenates one or more diffusion images.

app-mergeroi

app-mergetck

Merge multiple TCK files into one TCK file.

app-mp2rage-computet1andr1

Computes T1map and R1map images when provided a denoised mp2rage t1 image (see app-mp2rage-denoiseUNI).

app-mp2rage-denoiseuni

Removes noise in an MP2RAGE_UNI.nii.gz image given a user-provided regularization parameter (see app-mp2rage-selectregparam).

app-participant-report

App to generate report HTML for study participants

app-slicer-fsl

app-streamlinecategorysegmentation

app-temporary-renamelabels

app-tractanalysisprofiles

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

ashs-segment-validation

Code used to validate the efficacy and reliability of the ASHS Segmentation implementation on brainlife.io. For ASHS: http://picsl.upenn.edu/software/ashs/. For brainlife.io implementation: https://doi.org/10.25663/brainlife.app.262.

bcl

brainlife.github.io

brainlife.io home page

dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

devti_devhpcsubfields

This code was used to analyze the developmental trajectory of microstructural measures of white matter in hippocampal subfields.

devti_hpc2parietalcortex

Code written specifically for analyzing hpc2parietal tracks.

docs

Brainlife.io Documentation

floc

Functional localizer experiment used to define category-selective cortical regions

git-papers

learning-white-matter

lwx_devofverttracts

Source code for analysis steps

lwx_diffusion_bin

This is a set of scripts written to begin creating a preprocessing pipeline for diffusion data from children ages 4.5-8.5 years old and adults. They were created mainly for learning purposes. Refined versions of these scripts will be available in LWX_diffusion_preprocessing.

mp2rage-related-scripts

MP2RAGE Scripts - T1 map correction & Background noise removal

pestillilab_projects

This repository contains code beign developed for a majority of the projects being undertaken by the Pestilli Research Group.