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start [2011/04/15 02:12]
jochen replacing bad links with GUI links
start [2016/05/27 17:19] (current)
jochen [User's corner]
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 ====== NeuroElf wiki ====== ====== NeuroElf wiki ======
  
-{{:neuroelf_facelogo600.jpg?200 |NeuroElf logo }}Welcome to the NeuroElf wiki. If you would like to contribute, please read the information provided in the wiki internals section below, register and edit/add articles! :)+{{http://​neuroelf.net/​face.jpg?200 |NeuroElf logo}}Welcome to the NeuroElf wiki. If you would like to contribute, please read the information provided in the wiki internals section below, ​email register ​(at) neuroelf (dot) info, and once you get your user information,​ you can edit/add articles! :)
  
 Below you can find a preliminary and manually maintained table of contents. This means that in case you create a new article when you write up your own piece of documentation,​ please name it with a useful title, and if you consider the information you provide to be useful in a global context (e.g. a manual on how to use a specific tool or a solution to a general problem), please add the article to this page. Below you can find a preliminary and manually maintained table of contents. This means that in case you create a new article when you write up your own piece of documentation,​ please name it with a useful title, and if you consider the information you provide to be useful in a global context (e.g. a manual on how to use a specific tool or a solution to a general problem), please add the article to this page.
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   * [[Uploading image files]]   * [[Uploading image files]]
  
 +==== Matlab basics ====
 +  * [[Matlab - introduction|Introduction]]
 +  * [[Matlab - help|Help - where to find information on a topic?]]
 +  * [[Matlab - language|Matlab'​s language (basic vocabulary)]]
 +  * [[Matlab - datatypes|Variables,​ datatypes, and indexing]]
 +  * [[Matlab - expressions|Expressions]]
 +  * [[Matlab - precedence|Precedence - operators and identifiers]]
 +  * [[Matlab - M-files|M-files]]
 +  * [[Matlab - debugging|Debugging]]
 +  * [[Matlab - control structures|Control structures]]
 +  * [[Matlab - handles|Handles]]
 +  * [[Matlab - classes|Classes]]
 +  * [[Matlab - overloading|Overloading of functions and methods]]
 +  * [[Matlab - profiler|Profiler - cleaning up code]]
 ==== NeuroElf internals ==== ==== NeuroElf internals ====
   * [[NeuroElf introduction|Introduction]] (basic info, etc.)   * [[NeuroElf introduction|Introduction]] (basic info, etc.)
   * [[NeuroElf installation|Installation]] (instructions for both installer and flat folder/​snapshot ZIP)   * [[NeuroElf installation|Installation]] (instructions for both installer and flat folder/​snapshot ZIP)
   * [[NeuroElf MEX files|Compiling MEX files]] (some hints if compiling fails)   * [[NeuroElf MEX files|Compiling MEX files]] (some hints if compiling fails)
-  * [[NeuroElf changelog|Changelog]] (latest additions and changes to the toolbox)+  ​* [[NeuroElf release notes|Release notes]] (per-release list of substantial additions) 
 +  ​* [[NeuroElf changelog|Changelog]] (latest additions and changes to the snapshot of the toolbox)
   * [[NeuroElf features|List of features]] (attempt at a comprehensive overview)   * [[NeuroElf features|List of features]] (attempt at a comprehensive overview)
 +  * [[NeuroElf methods|Methods implemented in NeuroElf]] **(also contains citation references)**
   * [[NeuroElf support|Support]] (reporting errors and problems, [[NeuroElf feature requests|feature requests]])   * [[NeuroElf support|Support]] (reporting errors and problems, [[NeuroElf feature requests|feature requests]])
 +  * [[NeuroElf videos|Video tutorials]] (a set of screen-recordings showing various features of NeuroElf)
   * [[NeuroElf license|License and disclaimer]]   * [[NeuroElf license|License and disclaimer]]
  
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   * Model-based approaches (confirmatory,​ hypotheses driven): [[Processing stream - model creation|Model creation]], [[NeuroElf GUI - Compute multi-study glm|GLM regression]],​ [[NeuroElf GUI - Contrast manager|Contrast and correlation maps]], [[NeuroElf GUI - RFX mediation|Mediation analysis]]   * Model-based approaches (confirmatory,​ hypotheses driven): [[Processing stream - model creation|Model creation]], [[NeuroElf GUI - Compute multi-study glm|GLM regression]],​ [[NeuroElf GUI - Contrast manager|Contrast and correlation maps]], [[NeuroElf GUI - RFX mediation|Mediation analysis]]
   * Model-free approaches (exploratory,​ covariance-based/​multi-variate statistics):​ [[Processing stream - Cross-correlations|Cross-correlations]],​ [[Processing stream - ICA|ICA]], [[NeuroElf GUI - RFX mediation|Mediation analysis]]   * Model-free approaches (exploratory,​ covariance-based/​multi-variate statistics):​ [[Processing stream - Cross-correlations|Cross-correlations]],​ [[Processing stream - ICA|ICA]], [[NeuroElf GUI - RFX mediation|Mediation analysis]]
 +  * Meta-analyses:​ [[MKDA|Multi-level Kernel Density Analysis (MKDA)]]
   * Output visualization:​ [[Processing stream - map overlay|Map overlay]], [[neuroelf_gui - image montage ui|Montage creation]] (multi-slice display), [[Processing stream - surface projection|Surface projection]],​ [[Processing stream - flatmaps|Flatmaps]]   * Output visualization:​ [[Processing stream - map overlay|Map overlay]], [[neuroelf_gui - image montage ui|Montage creation]] (multi-slice display), [[Processing stream - surface projection|Surface projection]],​ [[Processing stream - flatmaps|Flatmaps]]
   * [[Processing stream - scripted|Scripted example]] (taken from my lab)   * [[Processing stream - scripted|Scripted example]] (taken from my lab)
 +
 +==== User's corner ====
 +  * [[ajay:​start|Ajay Satpute'​s]] [[ajay:​Neuroelf usage notes|usage notes]]
 +  * [[jochen:​start|Tips and tricks from the NeuroElf himself]]
  
 ===== Graphical User Interface (GUI) ===== ===== Graphical User Interface (GUI) =====
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   * [[neuroelf_gui - RFX mediation|RFX (single-level) mediation]] (Analysis menu)   * [[neuroelf_gui - RFX mediation|RFX (single-level) mediation]] (Analysis menu)
   * [[neuroelf_gui - ECG/GSR data analysis|ECG/​GSR data analysis]] (Analysis menu)   * [[neuroelf_gui - ECG/GSR data analysis|ECG/​GSR data analysis]] (Analysis menu)
 +  * [[neuroelf_gui - MKDA UI|Multi-level Kernel Density Analysis (MKDA)]] (Analysis menu -> Meta analysis)
   * [[neuroelf_gui - image montage ui|Image montage UI]] (Visualization menu)   * [[neuroelf_gui - image montage ui|Image montage UI]] (Visualization menu)
   * [[neuroelf_gui - rendering ui|Rendering UI]] (Visualization menu / render button)   * [[neuroelf_gui - rendering ui|Rendering UI]] (Visualization menu / render button)
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   * [[Attaching a protocol to a VTC|... attach a protocol to a VTC file]]?   * [[Attaching a protocol to a VTC|... attach a protocol to a VTC file]]?
   * [[Processing stream - quality_assessment|... assess fMRI data quality]]?   * [[Processing stream - quality_assessment|... assess fMRI data quality]]?
 +  * [[Close NeuroElf GUI after clear classes|... close the GUI after accidentally clearing everything?​]]
   * [[NeuroElf GUI - menu tree#​vmp_menu|... combine VMPs with the same spatial layout]]?   * [[NeuroElf GUI - menu tree#​vmp_menu|... combine VMPs with the same spatial layout]]?
   * [[Working with statistics|... compute a conjunction map]]?   * [[Working with statistics|... compute a conjunction map]]?
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   * MTC methods: [[mtc.ApplySSM|ApplySSM]],​ [[mtc.ApplyTSM|ApplyTSM]]   * MTC methods: [[mtc.ApplySSM|ApplySSM]],​ [[mtc.ApplyTSM|ApplyTSM]]
   * NTT methods: [[ntt.ChannelData|ChannelData]],​ [[ntt.Filter|Filter]],​ [[ntt.Resample|Resample]],​ [[ntt.SampleData|SampleData]]   * NTT methods: [[ntt.ChannelData|ChannelData]],​ [[ntt.Filter|Filter]],​ [[ntt.Resample|Resample]],​ [[ntt.SampleData|SampleData]]
-  * PLP methods: [[plp.PlotOnSlice|PlotOnSlice]],​ [[plp.PlotOnSurface|PlotOnSurface]]+  * PLP methods: ​[[plp.MKDA|MKDA]], ​[[plp.PlotOnSlice|PlotOnSlice]],​ [[plp.PlotOnSurface|PlotOnSurface]]
   * PRT methods: [[prt.ConvertToMS|ConvertToMS]],​ [[prt.ConvertToSingleTrial|ConvertToSingleTrial]],​ [[prt.ConvertToVol|ConvertToVol]],​ [[prt.CreateSDM|CreateSDM]],​ [[prt.SetDuration|SetDuration]],​ [[prt.ShiftOnsets|ShiftOnsets]]   * PRT methods: [[prt.ConvertToMS|ConvertToMS]],​ [[prt.ConvertToSingleTrial|ConvertToSingleTrial]],​ [[prt.ConvertToVol|ConvertToVol]],​ [[prt.CreateSDM|CreateSDM]],​ [[prt.SetDuration|SetDuration]],​ [[prt.ShiftOnsets|ShiftOnsets]]
   * SDM methods: [[sdm.AddFilters|AddFilters]],​ [[sdm.CalcBetas|CalcBetas]],​ [[sdm.ShowDesign|ShowDesign]]   * SDM methods: [[sdm.AddFilters|AddFilters]],​ [[sdm.CalcBetas|CalcBetas]],​ [[sdm.ShowDesign|ShowDesign]]
start.1302826320.txt.gz · Last modified: 2011/04/15 02:12 by jochen