====== ️Tools And Methods ======
also see "[[https://github.com/NPACore/awesome-neuroimaging|awesome-neuroimaging]]"

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

==== Magnetic Resonance Imaging (MRI) ====

  * [[tools:tat2|Time-averaged T2*]] - nT2* of BOLD EPI (fMRI), an [[tools:lncdtools|lncdtool]]
  * [[:tools:neuromelanin]]
  * [[tools:afni|AFNI]] ([[https://afni.nimh.nih.gov/|AFNI@NIMH]]) - suite of C, Python, R, & shell for the analysis and display of anatomical, functional and diffusion weighted data
  * [[tools:fsl]] ([[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki|FSL@Oxford]])  - tools for FMRI, MRI and diffusion brain imaging data
  * [[tools:freesurfer]] ([[https://surfer.nmr.mgh.harvard.edu/fswiki|FS@MGH]]) - information about running freesurfer for structural MRI data processing, segmentation, and surface generation
  * [[tools:rsfmri|Resting State MRI]]


  * [[:tools:motrak]] - motion awareness in MR simulation (proprietary sofware)
  * [[:tools:cifti surfaces]] - information about working with cortical surface files in R and with connectome workbench
  * [[:tools:BIDS apps]] - a list of useful software packages that work on BIDS-formatted data (BIDS apps) 

==== Magnetic Resonance Spectroscopy Imaging (MRSI) ====
  * [[grants:7t:mrsiacquisition|MRSI Acquisition]]
  * [[tools:hc|MRSI in HC @ 7T]]
  * [[tools:lcmodel|LC Model]]
  * [[tools:pfc|PFC ROI Placement]]


==== Electroencephalogram (EEG) ====
  * [[tools:loefeeg|EEG at Loeffler]]
  * [[tools:eeg_7t_preprocessingpipeline|EEG Preprocessing Pipeline for 7T/BrainMechR01]]
  * [[tools:spectralevents|Spectral Event Pipeline]]
  * [[tools:fooof]]
  * [[tools:snr]]
  * [[tools:eegCoordinates]]
  * [[tools:eeg_remark]]


==== Behavioral Tasks ====
  * [[tools:mgs|Memory Guided Saccade (MGS) Task]]
  * [[tools:antisaccade|Antisaccade Tasks]]
  * [[tools:habittask|Reward Learning and Habituation Task]]
  * [[tools:auditorysteadystate|Auditory Steady State]]
  * [[tools:daw|DAW Sequential Learning]]
  * [[:tools:rest]]

==== Samples ====
  * [[:tools:saliva]]
  * [[:tools:HairHormones]]
==== Statistical Methods ====
  * [[tools: Models that disaggregate between and within person effects]]
  * [[tools: Choosing k for age smooths in generalized additive models]]

==== Approaches to Increasing Sample Diversity during Image Acquisition/Analysis ====
  * Mitigating head motion: [[https://doi.org/10.1016/j.neuroimage.2018.01.023 | behavioral interventions (e.g., movie watching)]], [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731481/ | real-time motion feedback]], [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731481/| timeseries bagging]]
  * [[https://www.nature.com/articles/s41467-017-00908-7 | Sample weighting]]
  * [[https://bmcmedresmethodol.biomedcentral.com/articles/10.1186/s12874-018-0615-6 | 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)

==== Surveys and Assessments ====
  * [[tools: ADI]]
  * [[tools: STRAIN]]
  * [[tools:uppsp|UPPS-P Impulsivity Scale]]

==== Coding Languages and software tools ====
  * [[tools:r|R]] (used by R Studio)
  * [[:tools:shell]]
  * [[:tools:matlab]]
  * [[tools:python|]]
  * [[:tools:julia]]
  * [[:tools:wiki]]

==== Github ====
  * [[tools:Project reproducibility guides with gh-pages]]
  * [[:tools:bfg]]

==== General ====
  * [[tools:motrak]]
  * [[tools:lncdtools|LNCD Tools]]
  * [[tools:software|LNCD Software]]
  * [[tools:db|LNCD Database]]
  * [[tools:eyetracking|Eye Tracking]]
  * [[tools:make|make]]
  * [[tools:nic|NIC]]
  * [[tools:presentation|NeuroBS Presentation]]
  * [[tools:shell|Shell]]
  * [[tools:tidyverse|R:tidyverse/dplyr]]
  * [[tools:tutorials|Tutorials]]
  * [[tools:wormhole|Magic Wormhole]]
  * [[tools:lncdbot]]
  * [[tools:highresolutionlogos]]
  * [[tools:tmux]]


==== Wiki ====
  * [[tools:wiki:map|Wiki Map Description]]
  * [[tools:wiki:tricks|Wiki Tricks]]
  * [[tools:projectsTemplate]]

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=== Missing Pages ===
Linked from somewhere but the page doesn't exist yet ("orphans wanted").
~~NOCACHE~~
~~ORPHANSWANTED:wanted@tools~~