====== Manually updated contents page ======

Add pages in hierarchical manner here.


----

__Note:__ Some of instructions are organized via GoogleDocs DAG folder, assessable via yours or dag.labmember gmail account: 
https://drive.google.com/?authuser=0#folders/0B8170PnHBunGYzA2OGNjMTEtYTg5ZS00NzE4LTg1N2ItY2JlYTFhYzdiMmY3 

----

===== Lab organization =====

[[Lab-Organization:Lab-Organization_GoogleDrive]]

[[Lab-Organization:Lab-Organization_Calendars]]

[[Lab-Organization:Lab-Organization_Zotero_and_GitHub]]


===== BrainVoyager =====

[[BrainVoyager:BrainVoyager_Resources]]

[[BrainVoyager:BrainVoyager_Shortcuts]]

[[BrainVoyager:BrainVoyager_Install_On_Linux]]

[[BrainVoyager:BrainVoyager_Probabilistic_Maps]]

[[BrainVoyager:BrainVoyager_Surfaces]]

[[BrainVoyager:BrainVoyager_Dongles]]

[[BrainVoyager:BrainVoyager_TransformVMP]]

[[BrainVoyager:BrainVoyager_HumanAlignment]]

[[BrainVoyager:BrainVoyager_Contrasts]]

===== NeuroElf =====

[[NeuroElf:NeuroElf_resources]] Help and installation, DAG-specific bug fixes!

[[NeuroElf:NeuroElf_pipeline]]

[[NeuroElf:NeuroElf_based_functions]]

[[NeuroElf:NeuroElf_BrainVoyager]]

[[NeuroElf:NeuroElf_ToDo]]

[[NeuroElf:NeuroElf_pipeline_v2]]
===== JIP =====

http://www.nmr.mgh.harvard.edu/~jbm/jip/

[[JIP:JIP_Install_On_Linux_Gnome]]

===== Monkeypsych =====


[[Monkeypsych:Data_parameters]]

[[Monkeypsych:Monkeypsych_installation]]

[[Monkeypsych:Monkeypsych_changelog]]

[[Monkeypsych:Monkeypsych_todo]]

===== TDT =====

[[TDT:TDT_resources]]

[[TDT:TDT_status]]

[[TDT:TDT_ToDo]]

[[TDT:TDT_FAQ]]

===== MATLAB =====

[[MATLAB:MATLAB_Resources]]

[[MATLAB:MATLAB_helpful_hacks]]

[[MATLAB:MATLAB_documentation_guidelines]]

[[MATLAB:MATLAB_FieldTrip]]

[[MATLAB:MATLAB_PATH]]

===== Atlases =====

Anatomical atlases and other resources

[[Atlases:Atlases_resources]]

http://culhamlab.ssc.uwo.ca/fmri4newbies/primeroncorticalsulci.html

===== References =====

[[References:Zotero_instructions]]
===== Decision-Making =====

[[Decision-making:Decision-making_Resources]]

===== Git source control ======

[[Git:Git_Resources]]

[[Git:DAG_git_general_ideas]]

===== Links =====

Miscellaneous science-related links you would like to share (with brief description)

[[Links:Links_fMRI]]

[[Links:Links_ephys]]

[[Links:Links_statistics]]

[[Links:Links_fun]]

===== Linux =====

[[Linux:Linux_hacks]]

===== Setups =====

[[Setups:Setup1]]

[[Setups:Setup2]]

[[Setups:Setup3]]

[[Setups:UMG psychophysics setup]]

[[Setups:DPZ MRI setup]]


===== ePhys pipeline =====

[[ePhys pipeline:1) Pipeline overview]]

[[ePhys pipeline:2) Synchronization]]

[[ePhys pipeline:3) phys_gui]]

[[ePhys pipeline:4) Sorting]]

[[ePhys pipeline:5) Meta-info]]

[[ePhys pipeline:6) TDT Trial structure]]

[[ePhys pipeline:7) ToDo]]

[[ePhys pipeline:8) External links]]




===== spike analysis pipeline =====

[[spike analysis pipeline:Pipeline overview]]

[[spike analysis pipeline:Interaction with other pipelines]]

[[spike analysis pipeline:Keys]]

[[spike analysis pipeline:Defining conditions]]

[[spike analysis pipeline:Space definition]]

[[spike analysis pipeline:Statistics and tuning table]]

[[spike analysis pipeline:Population matfile format]]

[[spike analysis pipeline:Population analysis:Population PSTHs]]




===== Setup installation guides =====

[[Setups:Setup installation guides:eye tracker]]

[[Setups:Setup installation guides:parallel port]]

[[Setups:Setup installation guides:DAQ]]


===== Analysis =====

==== Stat ====

[[Analysis:Stat:FisherExactTest]]

[[Analysis:Stat:StatPower]]

[[Analysis:Stat:2DConfidenceEllipses]]

[[Analysis:Stat:MarkovChain]]

[[Analysis:Stat:ChiSquaredTest]]

[[Analysis:Stat:r-to-ZTransform]]

[[Analysis:Stat:ANOVA]]

[[Analysis:Stat:BayesFactor]]

==== fMRI ====

[[Analysis:fMRI:ExperimentalDesign]]

[[Analysis:fMRI:ActivationMaps]]

[[Analysis:fMRI:CollinearPredictors]]

[[Analysis:fMRI:SNR]]

[[Analysis:fMRI:AFNI]]

==== Spectral ====

[[Analysis:Spectral:SpectralResources]]

==== Planner ====

[[Planner:Planner_Installation]]

[[Planner:Planner_Usage]] 

===== 3DReco =====

[[3DReco:3DRecoResources]]

[[3DReco:angled_chamber_pipeline]]

===== MRI =====

[[MRI:PhysioMonitoring]]

===== waveclus =====

[[waveclus:output variables]]