freesurfer | Topic | Ecosyste.ms: Repos

Topic: "freesurfer"

freesurfer/freesurfer

Neuroimaging analysis and visualization suite

Language: C++ - Size: 946 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 669 - Forks: 257

aramis-lab/clinica

Software platform for clinical neuroimaging studies

Language: Python - Size: 35.1 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 244 - Forks: 85

raamana/visualqc

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

Language: Python - Size: 104 MB - Last synced at: 14 days ago - Pushed at: 10 months ago - Stars: 73 - Forks: 13

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 at: 6 months ago - Pushed at: about 4 years ago - Stars: 73 - Forks: 15

NYUMedML/DARTS

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

Language: Jupyter Notebook - Size: 37.8 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 69 - Forks: 24

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 at: 15 days ago - Pushed at: 5 months ago - Stars: 68 - Forks: 13

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 at: 6 days ago - Pushed at: about 1 year ago - Stars: 37 - Forks: 7

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: 113 MB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 23 - Forks: 7

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 at: 16 days ago - Pushed at: 7 months ago - Stars: 23 - Forks: 4

dipterix/three-brain-js

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

Language: JavaScript - Size: 32.3 MB - Last synced at: 28 days ago - Pushed at: about 2 months ago - Stars: 16 - Forks: 4

fphammerle/freesurfer-stats 📦

Python Library to Read FreeSurfer's Cortical Parcellation Anatomical Statistics

Language: Python - Size: 469 KB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 14 - Forks: 1

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 at: 29 days ago - Pushed at: 29 days ago - Stars: 13 - Forks: 2

dfsp-spirit/NeuroFormats.jl

Handling of structural neuroimaging file formats for Julia.

Language: Julia - Size: 6.23 MB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 12 - Forks: 2

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 at: about 2 years ago - Pushed at: over 5 years ago - Stars: 11 - Forks: 6

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 at: about 9 hours ago - Pushed at: over 2 years ago - Stars: 10 - Forks: 1

freesurfer/AutomatedFreeSurfer

Language: Shell - Size: 140 KB - Last synced at: 16 days ago - Pushed at: 6 months ago - Stars: 9 - Forks: 1

rcruces/MRI_analytic_tools

Pipelines and tools for MRI analysis

Language: HTML - Size: 2.97 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 8

fphammerle/freesurfer-surface 📦

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

Language: Python - Size: 3.84 MB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 0

dfsp-spirit/freesurfer_parallel_scripts

Shell scripts to run FreeSurfer's recon-all in parallel on multi-core machines. Developed during my time in Christine Ecker's Lab at KGU.

Language: Shell - Size: 309 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 8 - Forks: 3

dfsp-spirit/neuroformats-rs

Handling of structural neuroimaging file formats for Rust.

Language: Rust - Size: 17.4 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 7 - Forks: 1

dfsp-spirit/libfs

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

Language: C++ - Size: 41.2 MB - Last synced at: 15 days ago - Pushed at: 11 months ago - Stars: 7 - Forks: 0

SandraKla/ShinySurfer

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

Language: R - Size: 4.9 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 7 - Forks: 0

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 at: 22 days ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 0

aramis-lab/clinica-pydra-freesurfer

Pydra tasks for FreeSurfer designed for Clinica

Language: Python - Size: 299 KB - Last synced at: 5 days ago - Pushed at: 12 months ago - Stars: 5 - Forks: 1

fphammerle/freesurfer-volume-reader 📦

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

Language: Python - Size: 963 KB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1

dfsp-spirit/regfusionr

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

Language: R - Size: 99 MB - Last synced at: 15 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 1

ilwoolyu/SphericalLabeling

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

Language: Python - Size: 36.1 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 1

mwegrzyn/hiddenIdentityOfFaces

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

Language: Jupyter Notebook - Size: 75.7 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 0

shawntz/fmri

a (work in progress) attempt to transform the stanford memory lab's internal fmri preprocessing scripts into a generalizable template for consistency within and across lab projects

Language: Shell - Size: 286 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 2 - Forks: 0

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 at: 22 days ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

pegasus-isi/freesurfer-osg-workflow

A Pegasus workflow for running FreeSurfer on the Open Science Grid

Language: Python - Size: 13 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 3

flywheel-apps/freesurfer-recon-all

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

Language: Shell - Size: 37.2 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 2

jingyunc/ntools_browser

Web-based Electrode Visualization

Language: Jupyter Notebook - Size: 53.2 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 4

dfsp-spirit/anonsurfer

Anonymization of freesurfer output based on metadata dropping and defacing.

Language: Shell - Size: 149 KB - Last synced at: 22 days ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 1

davidj-brewster/autoneurosegment

DiCOM to NiFTI processing pipeline orchestration, combining multiple planes via ANTs to maximise resolution and suitability for clustering and post-processing

Language: Shell - Size: 272 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 1 - Forks: 0

davidj-brewster/agentic-e2e-dicom-medical-pipeline

Multi-Agentic adaptive FreeSurfer/FSL Registration, ROI-detection, Segmentation, Clustering, Visualisation and Anomaly detection System for DiCOM and NiFTi images and sequences

Language: Python - Size: 273 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

hiroshiban/FS2BV

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

Language: MATLAB - Size: 9.64 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

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 at: 22 days ago - Pushed at: about 3 years ago - Stars: 1 - 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 at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 2

sssilvar/docker_enigma_shape

Language: Mercury - Size: 12.9 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 2

aboualiaa/freesurfer Fork of freesurfer/freesurfer

Neuroimaging analysis and visualization suite

Language: C++ - Size: 755 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

dipterix/ieegio

File input output for neuroscience study

Language: R - Size: 57.1 MB - Last synced at: 28 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

Maddi5/FreeSurfer-FastSurfer_Comparison

This repository contains the scripts to perform the comparison between FreeSurfer and FastSurfer segmentations

Language: TeX - Size: 48.4 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

mcvinding/mri_stuff

Various helper functions for processing MRI for MEG analysis

Language: Shell - Size: 81.1 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

SlicerCBM/SlicerFreeSurferCommands

Run FreeSurfer commands within 3D Slicer

Language: Python - Size: 3.36 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

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 at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0