️Tools And Methods

also see “awesome-neuroimaging”

This (:tools) namespace includes what would be in the methods section of a paper. The companion :brain namespace includes what would be in the results section. see :brain vs :tools

• Time-averaged T2* - nT2* of BOLD EPI (fMRI), an lncdtool
• Neuromelanin
• AFNI (AFNI@NIMH) - suite of C, Python, R, & shell for the analysis and display of anatomical, functional and diffusion weighted data
• fsl (FSL@Oxford) - tools for FMRI, MRI and diffusion brain imaging data
• freesurfer (FS@MGH) - information about running freesurfer for structural MRI data processing, segmentation, and surface generation
• Resting State MRI

• MoTrak - Loeffler Simulator Motion Tracking - motion awareness in MR simulation (proprietary sofware)
• Surface-based Analysis (cifti) - information about working with cortical surface files in R and with connectome workbench
• BIDS apps - a list of useful software packages that work on BIDS-formatted data (BIDS apps)

• MRSI Acquisition
• MRSI in HC @ 7T
• LC Model
• PFC ROI Placement

• EEG at Loeffler
• EEG Preprocessing Pipeline for 7T/BrainMechR01
• Spectral Event Pipeline
• Fitting Oscillations and 1/f (FOOOF)
• Signal to Noise Ratio (SNR)
• EEG Coordinates
• EEG Remarking Status Channel

• Memory Guided Saccade (MGS) Task
• Antisaccade Tasks
• Reward Learning and Habituation Task
• Auditory Steady State
• DAW Sequential Learning
• Resting State Task

• saliva
• Hair Hormones

• Models that disaggregate between and within person effects
• A Practical Guide to Choosing the Value of k for Age Smooths in Generalized Additive (Mixed) Models

• Mitigating head motion: behavioral interventions (e.g., movie watching), real-time motion feedback, timeseries bagging
• Sample weighting
• Multiple imputation
• Non-US publically available developmental datasets: Chinese Color Nest Project, Brazilian High Risk Cohort, Drakenstein Child Health Study, Growing Up in Singapore Torwards Healthy Outcomes. Non-US collected but not available imaging datasets (collaboration): BrainTime (Netherlands), YOUth (Netherlands), KaessGroup (Germany), c-VEDA (UK, India), CBD (China), NESDA (Netherlands), Betula (Sweden), Barbi (China)

• Area Deprivation Index (ADI)
• Stress & Adversity Inventory
• UPPS-P Impulsivity Scale

• R (used by R Studio)
• Shell
• matlab
• Python
• julia
• Wiki (tool)

• Creating a Reproducibility Guide using Github Pages
• BFG: git Repo Cleaner

• MoTrak - Loeffler Simulator Motion Tracking
• LNCD Tools
• LNCD Software
• LNCD Database
• Eye Tracking
• make
• NIC
• NeuroBS Presentation
• Shell
• R:tidyverse/dplyr
• Tutorials
• Magic Wormhole
• LNCD Bot
• highresolutionlogos
• tmux

• Wiki Map Description
• Wiki Tricks
• Project Template

Linked from somewhere but the page doesn't exist yet (“orphans wanted”).