GitHub topics: fsl
andrewjahn/AndysBrainBook
This repository contains the files that generate Andy's Brain Book on ReadTheDocs.
Size: 877 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 197 - Forks: 73
aramis-lab/clinica
Software platform for clinical neuroimaging studies
Language: Python - Size: 35.4 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 258 - Forks: 88
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: 479 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 0
vanandrew/brainextractor
Brain Extraction Tool in Python
Language: Python - Size: 43 KB - Last synced at: 18 days ago - Pushed at: 6 months ago - Stars: 42 - Forks: 6
rhzxg/fluffsl
Unofficial VSCode syntax highlighting extension for The-Forge Shading Language (FSL)
Language: TypeScript - Size: 1.93 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 0 - Forks: 0
shimming-toolbox/shimming-toolbox
Code for performing static, dynamic and real-time shimming using external and internal MRI shim coils
Language: Python - Size: 1.78 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 39 - Forks: 14
Hyedryn/elikopy
ElikoPy is Python library aiming at easing the processing of diffusion imaging for microstructural analysis.
Language: Python - Size: 4.52 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 18 - Forks: 5
Macatools/macapype
PNH segmentation pipelines based on nipype
Language: Python - Size: 71.8 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 24 - Forks: 13
muschellij2/fslr
FSL-R Interface package
Language: R - Size: 19.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 41 - Forks: 11
GravO8/CT-preprocess
Preprocess head CT scans using python!
Language: Python - Size: 7.81 KB - Last synced at: 30 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0
hgresseau/ASL-Processing-with-ANTs
Guide to perform cerebral blood flow (CBF) processing on an arterial spin labelling (ASL) image with ANTs and FSL. The required codes are provided and explained.
Language: MATLAB - Size: 232 KB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 1
DVS-Lab/general
General utility scripts, documentation, and analysis tutorials for Smith Lab.
Language: Shell - Size: 63.5 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 4
kedar-codes/hippo_morph
Current code for my hippocampal morphometry workflow, based on the hippodeep_pytorch segmentation program and the SlicerSALT shape analysis software.
Language: Python - Size: 182 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 1
carpentries-incubator/SDC-BIDS-dMRI
Introduction to dMRI
Language: Jupyter Notebook - Size: 48.3 MB - Last synced at: 1 day ago - Pushed at: 5 days ago - Stars: 26 - Forks: 19
isamo09/fls-online-saves
client and server for storing local FLS saves for gta Online
Language: Python - Size: 35.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 2
umn-milab/qmri-ald
Image analysis pipelines of qunatitative MRI (qMRI), including diffusion MRI (dMRI), in patients with adrenoleukodystrophy (ALD)
Language: MATLAB - Size: 559 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
NatLee/nipype-preprocess-on-brain-MR
The project is used to do preprocessing on brain MR images by using Nipype.
Language: Python - Size: 3.63 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 37 - Forks: 7
alyxshang/shangshield.ml
An OCaml package to measure the security of passwords. :dragon: :camel:
Language: OCaml - Size: 6.84 KB - Last synced at: 3 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0
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: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0
mcclaskey/batch_fslstats
Small set of functions that use FSL to calculate mean values of .nii files. Works quickly on large datasets, on any operating system. Designed for users of all levels.
Language: Python - Size: 493 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
LaSEEB/structural-connectivity
Code to create structural connectivity matrix from preprocessed DWI and structural MRI data.
Language: Shell - Size: 19.5 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - 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: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0
Raciti/Fine-Prepro
Preprocessing of MRI for better use in medical tools or AI activities.
Language: Python - Size: 12 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
Arash-Keshavarz/Advanced_Computer_Vision
Exploring advanced computer vision concepts through simple yet insightful projects.
Language: Jupyter Notebook - Size: 2.93 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
lamyj/erwin
Quantitative MRI toolbox in Python
Language: Python - Size: 4.73 MB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 12 - Forks: 0
Strokzz/Gta5-Save
Size: 0 Bytes - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
adrialfonso/fsl-pydocker
FSL integration using Python and Docker. Streamline neuroimaging workflows with ease.
Language: Python - Size: 26.4 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 1
robertoostenveld/bids-tools
Tools for dealing with neuroimaging data in the BIDS structure
Language: Python - Size: 354 KB - Last synced at: 3 months ago - Pushed at: almost 7 years ago - Stars: 28 - Forks: 7
MJ12358/fsl-work-map
A Field Service Lightning map displaying service appointments or work orders and much more.
Language: JavaScript - Size: 4.49 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1
kasapakis-nk/bsc-thesis-mvpa-decoding-classification
Decoding and Classification of Category‐Specific Visual Stimuli in the Fusiform Gyrus Using fMRI Data and Machine Learning
Language: TeX - Size: 14.2 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
UniversumX/Omnidream
Simulation of optimal configurations of miniature TMS coils to encode information into the brain using Reinforcement Learning
Language: HTML - Size: 507 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
exlava/ALC-DTI
Alcohol study DTI Analyses
Language: Shell - Size: 3.08 MB - Last synced at: 5 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
wpmed92/WebMRI
An Emscripten port of BET and FLIRT of FMRIB Software Library
Language: C - Size: 67.4 MB - Last synced at: 7 days ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 1
pradhanhitesh/neuroimaging-resources
Language: Python - Size: 7.46 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
tambalostefano/lnifmri_prep
lnifmri_prep is a set of plain bash scripts to automate preprocessing and QC of fMRI data.
Language: Shell - Size: 5.81 MB - Last synced at: 11 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
angeella/pARI
pARI: permutation-based All-Resolutions Inference
Language: R - Size: 698 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0
IARSystems/ewrl78-bootloader
An example of a simple XMODEM serial bootloader for Renesas RL78
Language: C - Size: 98.6 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - 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: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
Jayveeeee24/iSpeak-Signs
Filipino Sign Language Learning Application with Static FSL Recognition
Language: Java - Size: 842 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
Omar-Saad-ELGharbawy/Investigating-Cognitive-Control-via-fMRI
Explore the neural basis of cognitive control with this repository's in-depth analysis of the Flanker Dataset using fMRI. Using bash scripting to streamline preprocessing and ROI analysis, while incorporating R scripts to explore brain region activity during the task.
Language: Shell - Size: 4.94 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
jennieablog/EnglishToSign
An automatic translation system from English text to Filipino Sign Language (FSL) using the E-Sign Approach
Language: JavaScript - Size: 31.3 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
aramis-lab/clinica-pydra-fsl
Pydra tasks for FSL designed for Clinica
Language: Python - Size: 241 KB - Last synced at: 21 days ago - Pushed at: 26 days ago - Stars: 3 - Forks: 1
mbedini/The-Mindboggle-101-atlas-in-FSL
A volumetric version of the Mindboggle 101 atlas conveniently imported in FSL. This repo was used in Bedini, M., Olivetti, E., Avesani, P., & Baldauf, D. (2023). Accurate localization and coactivation profiles of the frontal eye field and inferior frontal junction: an ALE and MACM fMRI meta-analysis. Brain Structure and Function, 1-21.
Size: 19.5 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
Ali-Mohammadnezhad/Diffusion-MRI-DTI-Preprocessing
Code snippets for preprocessing DTI/MRI neuroimaging data
Language: Shell - Size: 326 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
finchnSNPs/hyak-fsl
FSL container built for UW HYAK users
Language: Python - Size: 39.1 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
mbedini/The-HCP-MMP1.0-atlas-in-FSL
A volumetric version of the HCP-MMP1 atlas conveniently imported in FSL. This repo was used in Bedini, M., Olivetti, E., Avesani, P., & Baldauf, D. (2023). Accurate localization and coactivation profiles of the frontal eye field and inferior frontal junction: an ALE and MACM fMRI meta-analysis. Brain Structure and Function, 1-21.
Size: 353 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 2
0rC0/NeuroMet_MP2rage_pypes
Pipelines for structural analysis for NeuroMet Project
Language: Jupyter Notebook - Size: 232 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1
jhuguetn/fsl_oxford_asl-docker
FSL oxford_asl Docker image
Language: Dockerfile - Size: 17.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
wmotte/ocd
Scripts to process preclinical obsessive compulsive disorder data
Language: R - Size: 7.27 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 2
spunt/bspm
Utility MATLAB functions and wrappers for fMRI data analysis, mostly based in SPM12
Language: Matlab - Size: 419 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 20 - Forks: 17
IBT-FMI/SAMRI
Small Animal Magnetic Resonance Imaging via Python.
Language: Python - Size: 5.56 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 42 - Forks: 27
agdamsbo/normalisation-pipeline
Normalising T1 weighted brain scans and lesions.
Language: HTML - Size: 2.83 MB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
jlohmeier/atlasBREX
atlasBREX: Automated averaged template-derived brain extraction in animal MRI
Language: Shell - Size: 11.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 2
MJ12358/fsl-resource-calendar
A Field Service Lightning calendar displaying service resources and their service appointments.
Language: JavaScript - Size: 1.26 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1
maartenmennes/ICA-AROMA
ICA-AROMA Software Package: a data-driven method to identify and remove head motion-related artefacts from functional MRI data.
Language: Python - Size: 405 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 84 - Forks: 52
labhstats/lbhs_stroke_seg_manuals
A repository for supplementary considerations required to run certain stroke segmentation algorithms
Language: R - Size: 35.2 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0
spisakt/pTFCE
Probabilistic Threshold-Free Cluster Enhancement of Neuroimages
Language: R - Size: 42.1 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 35 - Forks: 6
nmningmei/preprocessing_pipelines
Preprocessing Pipelines for EEG (MNE-python), fMRI (nipype), MEG (MNE-python/autoreject) data
Language: Jupyter Notebook - Size: 2.29 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 21 - Forks: 4
IARSystems/ewrl78-linker-config-flashlibs
A collection of ILINK linker configurations that simplify project setup for flash libraries on IAR Embedded Workbench for Renesas RL78
Size: 398 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 1
weikanggong/Resting-state-fMRI-preprocessing
A Matlab-based software package for preprocessing the resting-state fMRI data
Language: MATLAB - Size: 4.31 MB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 8 - Forks: 6
dmascali/mni2atlas
FSL Anatomical Labels for MNI Vector/ROI
Language: MATLAB - Size: 38.8 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 16 - Forks: 3
quqixun/BrainPrep 📦
Preprocessing pipeline on Brain MR Images through FSL and ANTs, including registration, skull-stripping, bias field correction, enhancement and segmentation.
Language: Python - Size: 43.7 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 172 - Forks: 51
jennieablog/signtyper
A web application for documenting signs in Filipino Sign Language (FSL).
Language: JavaScript - Size: 36.1 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1
katochnitish/MRCI-Preproc
Language: Shell - Size: 30.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0
andrewrosss/nipype-generate-fieldmaps
Nipype workflow to generate fieldmaps from EPI acquisitions with differing phase-encoding directions
Language: Python - Size: 175 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
dangom/icicle-tree-melodic
Icicle tree to visualize the variance explained by each IC component, as output from MELODIC.
Language: Python - Size: 34.2 KB - Last synced at: 5 days ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0
rmukh/basicregistrationMRIpipeline
The basic structural and diffusion MRI registration with pre-processing pipeline in Python.
Language: Python - Size: 70.3 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
zavaro/fsl_slurm
A modified FSL version for use with Slurm
Language: Shell - Size: 24.7 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 3
chris-langfield/fslfeatsetup
Python library for setting up FEAT analyses (FSL)
Language: Python - Size: 432 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0
rlin27/BATMANN
Implementation for paper "BATMANN: A Binarized-All-Through Memory-Augmented Neural Network for Efficient In-Memory Computing"
Language: Python - Size: 54.6 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 0
Atharva-Phatak/One-Shot-Art
Using one shot learning to classify paintings
Language: Jupyter Notebook - Size: 5.29 MB - Last synced at: about 1 month ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 1
PTDZ/deface
A simple script to deface (with use of fsl_deface) multiple T1/T2-weighetned files prepared according to the BIDS standard.
Language: Shell - Size: 4.88 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
fcayci/xilinx_vga_fsl_ip_core
Example VGA IP Core using FSL for Xilinx FPGAs
Language: VHDL - Size: 199 KB - Last synced at: over 2 years ago - Pushed at: over 11 years ago - Stars: 5 - Forks: 1
sxg/Reg
CLI for 4D image registration of .mat file using the FMRIB Software Library's FNIRT tool.
Language: Python - Size: 85.9 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
p3proc/p3 📦
An extensible fMRI Preprocessing Pipeline in nipype based on a 2015 Jonathan Power Pipeline
Language: Python - Size: 4.73 MB - Last synced at: 5 days ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
carlossantosgarcia/few-shot-classification
We explore different techniques to perform few-shot-classification of fashion images.
Language: Jupyter Notebook - Size: 6.04 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1
NIRALUser/CIVILITY
Cloud Based Interactive Visualization of Tractography Brain Connectome (CIVILITY) is an interactive visualization tool of brain connectome in the web.
Language: JavaScript - Size: 35.5 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 4
jennieablog/syntheticfsl
A database application for signing exact English in Filipino Sign Language (FSL) using the JASigning virtual signing system that sythesises natural sign language performance using virtual human characters.
Language: JavaScript - Size: 38.6 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 1
schluppeck/dockerize-analysis
build a container from which EH's analysis code (and others) can be run, without relying on windows/mac compatibility
Language: Dockerfile - Size: 1.45 MB - Last synced at: 6 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1
andrewrosss/nipype-fsl-anat
Nipype interface(s) wrapping the fsl_anat command line tool
Language: Python - Size: 58.6 KB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1
arpitmaheshwari213/Epitome-Extraction-and-Tumour-Classification-from-MRIs-of-Brain
A CNN based classification model for 3D NIfTI MRIs of the brain.
Language: Python - Size: 8.75 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
omerferhatt/bold-fmri-img-processing
Preprocessing fMRI scans, localizing the brain area that processes faces.
Language: Python - Size: 16.6 KB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0
lucasfr/DrawEM_docker
This is an experimental Docker image containing MIRTK, DrawEM, and FSL.
Language: Dockerfile - Size: 14.6 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
mabast85/eddy_qc_release
Automated quality control tools for diffusion MRI data
Language: Python - Size: 1.07 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1
afiliot/BRATS-preprocessing
Reproduce BRATS preprocessing for a given patient (needed: 4 modalities T1, T2, T1c and FLAIR, optional: segmentation).
Language: Shell - Size: 3.91 KB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
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 at: 6 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
StoneCypher/fsl_traffic_light_ukrainian
The FSL traffic light example, translated to Ukrainian by @miles91
Size: 1000 Bytes - Last synced at: 3 months ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 0
