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tools [2023/10/27 12:40] – [General] willtools [2026/04/23 12:36] (current) – [General] martineza10
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 ====== ️Tools And Methods ====== ====== ️Tools And Methods ======
 also see "[[https://github.com/NPACore/awesome-neuroimaging|awesome-neuroimaging]]" 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) ==== ==== Magnetic Resonance Imaging (MRI) ====
  
   * [[tools:tat2|Time-averaged T2*]] - nT2* of BOLD EPI (fMRI), an [[tools:lncdtools|lncdtool]]   * [[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: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: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]]) - package for the analysis and visualization of structural and functional neuroimaging 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: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) ==== ==== Magnetic Resonance Spectroscopy Imaging (MRSI) ====
-  * [[tools:acquisition|MRSI Acquisition]]+  * [[grants:7t:mrsiacquisition|MRSI Acquisition]]
   * [[tools:hc|MRSI in HC @ 7T]]   * [[tools:hc|MRSI in HC @ 7T]]
   * [[tools:lcmodel|LC Model]]   * [[tools:lcmodel|LC Model]]
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 ==== Electroencephalogram (EEG) ==== ==== Electroencephalogram (EEG) ====
   * [[tools:loefeeg|EEG at Loeffler]]   * [[tools:loefeeg|EEG at Loeffler]]
-  * [[tools:preprocessingpipeline|EEG Preprocessing Pipeline for 7T/BrainMechR01]]+  * [[tools:eeg_7t_preprocessingpipeline|EEG Preprocessing Pipeline for 7T/BrainMechR01]]
   * [[tools:spectralevents|Spectral Event Pipeline]]   * [[tools:spectralevents|Spectral Event Pipeline]]
-  * [[tools:fooof|FOOOF]]+  * [[tools:fooof]] 
 +  * [[tools:snr]] 
 +  * [[tools:eegCoordinates]] 
 +  * [[tools:eeg_remark]]
  
  
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   * [[tools:habittask|Reward Learning and Habituation Task]]   * [[tools:habittask|Reward Learning and Habituation Task]]
   * [[tools:auditorysteadystate|Auditory Steady State]]   * [[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 ==== ==== Coding Languages and software tools ====
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   * [[tools:python|]]   * [[tools:python|]]
   * [[:tools:julia]]   * [[:tools:julia]]
 +  * [[:tools:wiki]]
 +  * [[:tools:zenodo]]
  
 +==== Github ====
 +  * [[tools:Project reproducibility guides with gh-pages]]
   * [[:tools:bfg]]   * [[:tools:bfg]]
 +
 ==== General ==== ==== General ====
 +  * [[tools:geocode]]
   * [[tools:motrak]]   * [[tools:motrak]]
   * [[tools:lncdtools|LNCD Tools]]   * [[tools:lncdtools|LNCD Tools]]
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   * [[tools:wormhole|Magic Wormhole]]   * [[tools:wormhole|Magic Wormhole]]
   * [[tools:lncdbot]]   * [[tools:lncdbot]]
 +  * [[tools:highresolutionlogos]]
 +  * [[tools:tmux]]
  
  
 ==== Wiki ==== ==== Wiki ====
-  * [[tools:wikimap|Wiki Map Description]] +  * [[tools:wiki:map|Wiki Map Description]] 
-  * [[tools:wikitricks|Wiki Tricks]]+  * [[tools:wiki:tricks|Wiki Tricks]] 
 +  * [[tools:projectsTemplate]]
  
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