freesurfer/freesurfer

Neuroimaging analysis and visualization suite

Language: C++ - Size: 760 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 550 - Forks: 236

aramis-lab/clinica

Software platform for clinical neuroimaging studies

Language: Python - Size: 33.9 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 216 - Forks: 71

cfatuesta/AutomatedFreeSurfer

Language: Shell - Size: 121 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 6 - Forks: 1

dfsp-spirit/brainloc

Given a brain coordinate or cluster in MNI305 space, compute MNI152 and Talairach coordinates and find the closest brain regions.

Language: R - Size: 4.49 MB - Last synced: 25 days ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

dfsp-spirit/anonsurfer

Anonymization of freesurfer output based on metadata dropping and defacing.

Language: Shell - Size: 149 KB - Last synced: 25 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 1

dfsp-spirit/freesurferformats

GNU R package for reading and writing neuroimaging file formats. Not limited to FreeSurfer anymore, despite its name.

Language: R - Size: 7.47 MB - Last synced: 24 days ago - Pushed: 4 months ago - Stars: 23 - Forks: 3

aramis-lab/clinica-pydra-freesurfer

Pydra tasks for FreeSurfer designed for Clinica

Language: Python - Size: 299 KB - Last synced: 8 days ago - Pushed: 26 days ago - Stars: 5 - Forks: 1

dfsp-spirit/fsbrain

R library for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.

Language: R - Size: 375 MB - Last synced: 24 days ago - Pushed: 4 months ago - Stars: 59 - Forks: 12

raamana/graynet

Subject-wise networks from structural MRI, both vertex- and voxel-wise features (thickness, GM density, curvature, gyrification)

Language: Jupyter Notebook - Size: 33.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 34 - Forks: 7

dfsp-spirit/freesurfer_parallel_scripts

Shell scripts to run FreeSurfer's recon-all in parallel on multi-core machines.

Language: Shell - Size: 264 KB - Last synced: 25 days ago - Pushed: 11 months ago - Stars: 7 - Forks: 3

raamana/visualqc

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.

Language: Python - Size: 104 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 72 - Forks: 13

dfsp-spirit/neuroformats-rs

Handling of structural neuroimaging file formats for Rust.

Language: Rust - Size: 8.65 MB - Last synced: 25 days ago - Pushed: about 1 month ago - Stars: 6 - Forks: 1

dfsp-spirit/neuro

Go module for reading and writing structural neuroimaging file formats. Supports FreeSurfer MGH, MGZ, and related formats.

Language: Go - Size: 8.02 MB - Last synced: 25 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

jingyunc/ntools_browser

Web-based Electrode Visualization

Language: Jupyter Notebook - Size: 53.2 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 2 - Forks: 4

dfsp-spirit/abide_preproc_smri_freesurfer6

Data from our own pre-processing of the ABIDE I sMRI dataset (1035 subjects) in FreeSurfer v6.

Size: 1.7 MB - Last synced: 25 days ago - Pushed: 11 months ago - Stars: 4 - Forks: 0

Qoala-T/QC

Qoala-T is a supervised-learning tool for quality control of FreeSurfer segmented MRI data

Language: R - Size: 16.6 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 72 - Forks: 14

pegasus-isi/freesurfer-osg-workflow

A Pegasus workflow for running FreeSurfer on the Open Science Grid

Language: Python - Size: 13 MB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 2 - Forks: 3

0rC0/NeuroMet_MP2rage_pypes

Pipelines for structural analysis for NeuroMet Project

Language: Jupyter Notebook - Size: 232 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

dfsp-spirit/libfs

A header-only, no-dependency, C++11 library for accessing FreeSurfer neuroimaging file formats.

Language: C++ - Size: 40.6 MB - Last synced: 25 days ago - Pushed: 3 months ago - Stars: 6 - Forks: 0

dipterix/three-brain-js

Javascript engine for 3D brain model (used by RAVE project)

Language: JavaScript - Size: 38.7 MB - Last synced: 22 days ago - Pushed: about 2 months ago - Stars: 11 - Forks: 4

mcvinding/mri_stuff

Various helper functions for processing MRI for MEG analysis

Language: Shell - Size: 81.1 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

NYUMedML/DARTS

Code for DARTS: DenseUnet-based Automatic Rapid Tool for brain Segmentation

Language: Jupyter Notebook - Size: 37.8 MB - Last synced: 5 months ago - Pushed: 7 months ago - Stars: 66 - Forks: 24

dfsp-spirit/brainload

A python module designed to reduce your brain load while accessing FreeSurfer brain surface and morphometry data files of single subjects and groups.

Language: Python - Size: 102 MB - Last synced: 25 days ago - Pushed: over 1 year ago - Stars: 9 - Forks: 1

elidom/Cortical-Thickness

This is where I describe the surface-based cortical thickness workflows that I have learned to use.

Language: Shell - Size: 4.08 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 1

fphammerle/freesurfer-stats 📦

Python Library to Read FreeSurfer's Cortical Parcellation Anatomical Statistics

Language: Python - Size: 469 KB - Last synced: 26 days ago - Pushed: about 1 year ago - Stars: 12 - Forks: 1

sssilvar/docker_enigma_shape

Language: Mercury - Size: 12.9 MB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 1 - Forks: 2

rcruces/MRI_analytic_tools

Pipelines and tools for MRI analysis

Language: HTML - Size: 2.97 MB - Last synced: 7 months ago - Pushed: 12 months ago - Stars: 9 - Forks: 8

npnl/PALS

Pipeline for Analysing Lesions after Stroke (PALS) is a scalable and user-friendly toolbox designed to facilitate standardised analysis and ensure quality in stroke research using T1-weighted MRIs

Language: Python - Size: 94.9 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 17 - Forks: 7

HaiyangJin/fMRI-Matlab

Matlab Wrapper of Surface-based Analysis. Custom Matlab functions for running analyses with FreeSurfer, CoSMoMVPA, HCP pipeline (and SamSrf)...

Language: MATLAB - Size: 171 MB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 11 - Forks: 2

micerr/Epilepsy-dMRI-VNS

Assessing microstructural brain differences in epileptic patients with vagus nerve stimulation via diffusion MRI, tractography and machine learning

Language: Jupyter Notebook - Size: 270 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

seantma/MADC-FileIO

Misc scripts for MADC fMRI images transfers and preprocessing

Language: Shell - Size: 8.61 MB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

fphammerle/freesurfer-volume-reader 📦

Python script & library to read hippocampal volumes computed by Freesurfer & ASHS

Language: Python - Size: 963 KB - Last synced: 4 days ago - Pushed: 11 months ago - Stars: 4 - Forks: 1

fphammerle/freesurfer-surface 📦

Python Library to Read and Write Surface Files in Freesurfer's TriangularSurface Format

Language: Python - Size: 3.84 MB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 8 - Forks: 0

SlicerCBM/SlicerFreeSurferCommands

Run FreeSurfer commands within 3D Slicer

Language: Python - Size: 3.36 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

dfsp-spirit/regfusionr

R implementation of registration fusion method for MNI152 - 305 mapping.

Language: R - Size: 99 MB - Last synced: 25 days ago - Pushed: over 1 year ago - Stars: 5 - Forks: 1

SandraKla/ShinySurfer

Software Tool for the Analysis and Visualization of MRI images of the brain

Language: R - Size: 4.9 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 7 - Forks: 0

ilwoolyu/SphericalLabeling

SphericalLabeling: Cortical Surface Labeling using Spherical Data Augmentation and Context-aware Training

Language: Python - Size: 36.1 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 5 - Forks: 1

flywheel-apps/freesurfer-recon-all

Gear that runs FreeSurfer v7.2.0 Release (July 19, 2021)

Language: Shell - Size: 37.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 2

aboualiaa/freesurfer Fork of freesurfer/freesurfer

Neuroimaging analysis and visualization suite

Language: C++ - Size: 755 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

MLMH-Lab/How-To-Build-A-Machine-Learning-Model

Code for Chapter 19 - A Step-By-Step Tutorial On How To Build A Machine Learning Model

Language: Jupyter Notebook - Size: 1.73 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 11 - Forks: 6

dfsp-spirit/NeuroFormats.jl

Handling of structural neuroimaging file formats for Julia.

Language: Julia - Size: 6.23 MB - Last synced: 17 days ago - Pushed: 10 months ago - Stars: 11 - Forks: 1

hiroshiban/FS2BV

A package to import FreeSurfer/SPM/FLS ROIs to BrainVoyager as VOIs/POIs.

Language: MATLAB - Size: 8.93 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

mwegrzyn/hiddenIdentityOfFaces

Data & Code for "The hidden identity of faces: A case of lifelong prosopagnosia"

Language: Jupyter Notebook - Size: 75.7 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 3 - Forks: 0

DEPREDICT/sphere2dice

Sphere2dice converts Cortical Brain Morphometry data from FreeSurfer or Gifty type into a stack of 2D images and saves is as numpy array. This stack of images is easier to use as input to conventional CNNs, while avoiding projection issues other methods suffer from.

Language: Python - Size: 7.67 MB - Last synced: 12 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

darwingr/MRIDB

A cross-platform desktop GUI for statistical/ML analysis of volumetric brain data processed from fMRI scans of over 4,000 juvenile patients.

Language: Java - Size: 22.3 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 2

kondratevakate/your-brain-mri-visualization

Use `freesurfer` to process your imaging data, and get fancy viz in `blender`

Language: Jupyter Notebook - Size: 24 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

SandraKla/ShinySurfer_Homepage

Homepage for ShinySurfer

Language: HTML - Size: 1.32 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

jun130/Brain_Age_Measurement

age of brain measurement as use FREESURFER tool

Language: Python - Size: 133 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

AdoNunes/CT_trajectory_features_ASD_2019

Age-related changes in Cortical Thickness in Autism

Language: MATLAB - Size: 69.3 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

sebastientourbier/connectomemapper-ubuntu16.04

Docker image that provides a Ubuntu 16.04 (Xenial) with all CMP pre-requisite software installed

Language: Dockerfile - Size: 32.2 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0