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start [2011/04/04 15:35] – changed link jochen | start [2012/10/05 14:41] – [wiki internals] jochen | ||
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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:// |
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, | 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, | ||
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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 - datatypes|Datatypes, | ||
+ | * [[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/ | * [[NeuroElf installation|Installation]] (instructions for both installer and flat folder/ | ||
* [[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 features|List of features]] (attempt at a comprehensive overview) | * [[NeuroElf features|List of features]] (attempt at a comprehensive overview) | ||
* [[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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* [[Processing stream - preprocessing|Configuration of preprocessing steps]] | * [[Processing stream - preprocessing|Configuration of preprocessing steps]] | ||
* [[Processing stream - recording experimental timing and behavior|Recording onsets and responses]] | * [[Processing stream - recording experimental timing and behavior|Recording onsets and responses]] | ||
- | * Model-based approaches (confirmatory, | + | * Model-based approaches (confirmatory, |
- | * Model-free approaches (exploratory, | + | * Model-free approaches (exploratory, |
+ | * Meta-analyses: | ||
* Output visualization: | * Output visualization: | ||
* [[Processing stream - scripted|Scripted example]] (taken from my lab) | * [[Processing stream - scripted|Scripted example]] (taken from my lab) | ||
+ | |||
+ | ==== User's corner ==== | ||
+ | * [[ajay: | ||
===== 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/ | * [[neuroelf_gui - ECG/GSR data analysis|ECG/ | ||
+ | * [[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# | * [[NeuroElf GUI - menu tree# | ||
* [[Working with statistics|... compute a conjunction map]]? | * [[Working with statistics|... compute a conjunction map]]? | ||
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* [[Neuroelf GUI - image montage UI|... create high-resolution images of overlaid maps on slice data]]? | * [[Neuroelf GUI - image montage UI|... create high-resolution images of overlaid maps on slice data]]? | ||
* [[Displaying the motion-parameters of a subject|... display the motion parameters of a subject]]? | * [[Displaying the motion-parameters of a subject|... display the motion parameters of a subject]]? | ||
- | * [[Timecourse plots|... extract and plot timecourse and trial-related averages]]? | + | * [[mdm.VOICondAverage|... extract and plot timecourse and trial-related averages]]? |
* [[Segmenting brains|... fine-tune brain segmentation]]? | * [[Segmenting brains|... fine-tune brain segmentation]]? | ||
* [[Processing stream - model creating|... generate PRT files in Matlab]]? | * [[Processing stream - model creating|... generate PRT files in Matlab]]? | ||
- | * [[SPM import - contrast maps|... import SPM contrast maps (convert SPM t- and F-maps to VMP format)]]? | + | * [[importvmpfromspms|... import SPM contrast maps (convert SPM t- and F-maps to VMP format)]]? |
- | * [[SPM import - regression results|... import SPM regression results (store SPM 1st level regression output in a RFX-GLM)]]? | + | * [[importrfxglmfromspms|... import SPM regression results (store SPM 1st level regression output in a RFX-GLM)]]? |
- | * [[SPM import - timecourse data|... import SPM timecourse data (convert SPM preprocessing output to VTC format)]]? | + | * [[importvtcfromanalyze|... import SPM timecourse data (convert SPM preprocessing output to VTC format)]]? |
* [[heartbeats|... perform ECG / heart-rate data analysis]]? | * [[heartbeats|... perform ECG / heart-rate data analysis]]? | ||
* [[GSR data analysis|... perform GSR data analysis]]? | * [[GSR data analysis|... perform GSR data analysis]]? | ||
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* MTC methods: [[mtc.ApplySSM|ApplySSM]], | * MTC methods: [[mtc.ApplySSM|ApplySSM]], | ||
* NTT methods: [[ntt.ChannelData|ChannelData]], | * NTT methods: [[ntt.ChannelData|ChannelData]], | ||
- | * PLP methods: [[plp.PlotOnSlice|PlotOnSlice]], | + | * PLP methods: |
* PRT methods: [[prt.ConvertToMS|ConvertToMS]], | * PRT methods: [[prt.ConvertToMS|ConvertToMS]], | ||
* SDM methods: [[sdm.AddFilters|AddFilters]], | * SDM methods: [[sdm.AddFilters|AddFilters]], | ||
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* SRF methods: [[srf.AddMarkers|AddMarkers]], | * SRF methods: [[srf.AddMarkers|AddMarkers]], | ||
* VMP methods: [[vmp.ClusterTable|ClusterTable]], | * VMP methods: [[vmp.ClusterTable|ClusterTable]], | ||
- | * VMR methods: [[vmr.ApplyTRF|ApplyTRF]], | + | * VMR methods: [[vmr.ApplyTRF|ApplyTRF]], [[vmr.CleanVMR|CleanVMR]], [[vmr.CreateVTC|CreateVTC]], |
* VOI methods: [[voi.AddSphericalVOI|AddSphericalVOI]], | * VOI methods: [[voi.AddSphericalVOI|AddSphericalVOI]], | ||
* VTC methods: [[vtc.Correlate|Correlate]], | * VTC methods: [[vtc.Correlate|Correlate]], | ||
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==== Data import ==== | ==== Data import ==== | ||
+ | * [[dcm2nii]] - import DICOM to NIftI format (using SPM's DICOM Import tool) | ||
+ | * [[dicom2nii]] - import DICOM or PAR/REC to NIftI format (no SPM required) | ||
* [[fmriqasheet]] - visualize the result of '' | * [[fmriqasheet]] - visualize the result of '' | ||
* [[fmriquality]] - fMRI quality assessment (per run, estimates measures of noise as well as motion and detects outliers) | * [[fmriquality]] - fMRI quality assessment (per run, estimates measures of noise as well as motion and detects outliers) | ||
+ | * [[importrfxglmfromspms]] - import several SPM.mat files (and the used timecourses) into BrainVoyager QX's [[xff - GLM format|RFX-GLM format]] | ||
+ | * [[importvmpfromspms]] - import several 3D SPM based t- or F-maps into BrainVoyager QX's [[xff - VMP format|VMP format]] | ||
* [[importvmrfromanalyze]] - import one 3D [[xff - NII format|Analyze/ | * [[importvmrfromanalyze]] - import one 3D [[xff - NII format|Analyze/ | ||
* [[importvtcfromanalyze]] - import several 3D or one 4D [[xff - NII format|Analyze/ | * [[importvtcfromanalyze]] - import several 3D or one 4D [[xff - NII format|Analyze/ |
start.txt · Last modified: 2016/05/27 15:19 by jochen