neuroelf_features
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— | neuroelf_features [2011/04/01 22:59] (current) – created jochen | ||
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+ | ====== NeuroElf Features ====== | ||
+ | While this list might not be complete, it tries to give an overview of what the NeuroElf toolbox can do (and, to some extent, what it cannot do), linking to other wiki pages containing information on how the user can achieve the required tasks with the toolbox. | ||
+ | |||
+ | Next to the purely file-operation ([[xff]] class to read and write file formats commonly used in fMRI data analyses) functionality, | ||
+ | |||
+ | ===== Data analysis ===== | ||
+ | * **limited** capabilities for **data import** with functions [[dcm2nii]] (DICOM to NIftI import via SPM5/8 code) or [[dicom2nii]] (import without SPM code, still not fully functional), | ||
+ | * **fMRI quality control** with [[fmriquality]] (computation) and [[fmriqasheet]] (assessment) | ||
+ | * **batched preprocessing** of fMRI data (re-using **SPM5/ | ||
+ | * attempting to **correct for magnetic field inhomogeneities** (intensity bias field) using the [[pmbfilter]] function or the [[vmr.InhomogeneityCorrect|VMR:: | ||
+ | * **reconstructing a segmentation** as a surface using the [[vmr.DBReco|VMR:: | ||
+ | * morph (**smoothing**, | ||
+ | * **SPM-to-BVQX data import** with [[importvtcfromanalyze]] (time courses), [[importvmpfromspms]] (maps), and [[importrfxglmfromspms]] (entire set of first-level stats) | ||
+ | * performing **robust regression** and computing t-statistics based on those results with the [[fitrobustbisquare]] (single sample regression), | ||
+ | * first-level regression (**beta-estimation**), | ||
+ | * **extract time-course data** from VTC files using either the [[vtc.VOITimeCourse|VTC:: | ||
+ | * VOI-based GLM computation (regression) using the [[mdm.ComputeVOIGLM]] method | ||
+ | * **single-run ICA** using the [[http:// | ||
+ | * RFX **contrast computation** and **correlation with (behavioral) covariates** using the [[NeuroElf GUI - contrast manager|Contrast Manager UI]] or the [[glm.RFX_tMap|GLM:: | ||
+ | * RFX **(single-level) mediation analysis** (whole-brain mediation mapping) using the [[NeuroElf GUI - RFX mediation|RFX mediation analysis]] dialog for data stored in [[xff - GLM format|BrainVoyager QX's GLM format]] (or the [[mediationpset]] function on the command line for extracted data) | ||
+ | * computing **[[Working with statistics|conjunction maps]]** | ||
+ | * estimating true-Null **cluster-size thresholds** using using [[alphasim - extended uses|alphasim]] | ||
+ | * classifying data with a Support-Vector-Machine **(SVM) classifier** using the [[svmtrain]] and [[svmpredict]] functions (which re-use the [[http:// | ||
+ | |||
+ | ===== Result generation ===== | ||
+ | * creating **cluster tables** with the [[NeuroElf GUI|main GUI]] or using the [[vmp.ClusterTable|VMP:: | ||
+ | * **extracting beta values** from clusters with the [[NeuroElf GUI|main GUI]] or using the [[glm.VOIBetas|GLM:: | ||
+ | |||
+ | ===== Data visualization ===== | ||
+ | * creating **high-resolution slice images** (overlaid statistics, montage images) using the [[NeuroElf GUI - image montage UI|Image Montage UI]], incl. multi-map overlay and integration into variable background | ||
+ | * creating **high-resolution surface images** (overlaid statistics) using the screenshot feature of the [[NeuroElf GUI]] satellite window | ||
+ | * visualizing activation maps as flatmaps using the files created by [[neuroelf_makefiles]] and the SMP sampling either via the [[NeuroElf GUI|main GUI]] or the [[vmp.CreateSMP|VMP:: | ||
+ | * creating **high-quality 3D renderings** of brains (incl. statistics) using the [[NeuroElf GUI - rendering UI|Rendering UI]] | ||
+ | * creating GLM **beta bar or scatter plots** using the [[NeuroElf GUI - GLM beta plotter|GLM beta plotter]] feature (supports subject groups and plotting of contrast values) | ||
+ | * creating **trial/ | ||
+ | * **flexible time-course plotting** using the [[tcplot]] function | ||
+ | * plotting of (conditional) **confidence ellipses** using the [[cellipse]] function | ||
+ | |||
+ | ===== Not (yet) implemented features ===== | ||
+ | * segmentation (only via SPM's preprocessing) | ||
+ | * inter-subject normalization (only via SPM's preprocessing) | ||
+ | * group-based ICA | ||
+ | * multi-level mediation analysis | ||
+ | * Granger Causality (network analysis and whole-brain mapping) | ||
+ | |||
+ | Please note, that at the moment I have too little time to develop and/or integrate these features into the toolbox! | ||
neuroelf_features.txt · Last modified: 2011/04/01 22:59 by jochen