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neuroelf_gui_-_mdm_voi_condition_average_ui [2011/04/03 05:22] (current)
jochen created
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 +====== NeuroElf - MDM VOI condition averages ======
 +
 +===== Motivation =====
 +While hypothesis testing usually is done via formulating a Null-hypothesis (e.g. no systematic effect of differential processing of conditions),​ for which then a probability is given that the data could have been obtained if the Null-hypothesis were true (and a small enough p-value leading to rejection of this Null-hypothesis in favor of an alternative explanation:​ the difference in condition leads to a meaningful effect), false-positives can (**and do!**) still occur frequently. As one additional piece of evidence, it can be of great value to assess whether the region of interest (functionally or anatomically defined, or even just a peak voxel) shows a typical response profile in case the effect is observed in a classical stimulus-driven experiment (different stimuli or instructions to stimuli are contrasted).
 +
 +One hopes to find a response shape (over time) that resembles the canonical response and, if such a shape is observed, one can have additional confidence in the findings (as opposed to observing more or less random fluctuations over time, which simply happened to "​subtract"​ to a "​significant"​ but possibly false-positive finding).
 +
 +===== Requirements =====
 +To use this feature in NeuroElf, the following files must be available:
 +
 +  * a [[xff - VOI format|VOI file]] must be loaded (using the load-clusters button in the [[NeuroElf GUI#​configured_clusters_and_table_output|cluster toolbar]])
 +  * [[xff - VTC format|VTC files]] of all runs of subjects which are to be included in the average plots
 +  * [[xff - PRT format|PRT files]] describing the onsets at which stimuli of different conditions were presented
 +  * an [[xff - MDM format|MDM file]] referencing those VTC and PRT files (**an MDM referencing SDM files will not work, given that the onsets are no longer available!**)
 +  * optionally referenced motion parameter files and temporal filtering settings in the ''​mdm.RunTimeVars''​ structure (see the [[xff#​auxiliary_functionality|Storing additional information]] sub-subsection of the xff class overview page)
 +
 +===== Invoking the UI =====
 +To bring up the condition-based averaging plot, **make sure the correct list of clusters** is being displayed in the list of VOIs/​clusters (the duration for the extraction roughly increases linearly with the number and size of clusters!), then select the ''​**Create VOI condition plots**''​ entry from the [[NeuroElf GUI - menu tree#​analysis_menu|Analysis menu]].
 +
 +Once an MDM is selected and loaded, NeuroElf will examine the protocol files and show a list of conditions found in those files for selection. This is a good time to remove any conditions of no interest (fixation and rating periods, active baseline, etc.) as this will speed up the subsequent computations.
 +
 +Next, the time courses will be extracted for all VOIs in all VTCs in the MDM file (subject selection is implemented at a later stage). This can take up to several minutes, depending on the number of VOIs and VTCs for which this has to be done.
 +
 +In case this is required by the settings (motion parameters and/or temporal filtering), design matrices will be created for the runs, so that time courses can be filtered.
 +
 +Eventually, a new UI appears.
 +
 +===== GUI layout =====
 +{{:​neuroelf_gui:​mdm_voi_condavg_plot.png|MDM VOI condition average plot (showing three conditions, with error bands representing RFX standard-error of the mean}}
 +
 +===== Controls =====
 +The following controls are available:
 +
 +  * Select cluster (dropdown): changes the currently shown VOI/cluster
 +  * Update position (checkbox): if checked sets the current position (and cluster, unless reloaded) in the main UI to the cluster peak coordinate
 +  * Grouping (dropdown) with settings **FFX**, **RFX**, and **RFX (weighted)**
 +    * FFX: error bands represent fixed-effects standard deviation (SD) or standard error (SE) of the mean
 +    * RFX: error bands represent random-effects SD or SE of the mean (an intermediate within-subject averaging step precedes any subsequent computation)
 +    * RFX (weighted): **//this is not yet implemented!!//​** this option shows a random-effects SD or SE, whereas outlier subjects are down-weighed
 +  * Select conditions (multi-selection listbox): the selected conditions will be averaged and plotted (one plotted line/band per selected condition)
 +  * Condition color settings (button): this button allows to re-set the colors for each condition (as they first appear in a referenced PRT file) for visualization purposes
 +  * Collapsed conditions (multi-selection listbox): the configured collapsings will be performed and averaged plots will be shown collapsed (one plotted line/band per selected collapsing)
 +  * Add collapsing (button): takes the currently selected conditions and creates a collapsing configuration (requesting a name), this in effect allows to combine onsets of several conditions at a late stage instead of having to re-create protocol files
 +  * Remove collapsing (button): removes the currently selected collapsings from the list
 +  * Collapsed conditions color settings (button): this button allows to define new colors for each collapsing
 +  * Selected groups (multi-selection listbox): if groups are configured in the ''​mdm.RunTimeVars.Groups''​ field (same syntax as with GLM group definition),​ sub-groups of subjects can be (de-) selected for visualization
 +  * Robust estimates (checkbox): if checked averages will be performed with outliers removed
 +  * SE instead of SD (checkbox): if checked (and error bands are visualized) error bands represent SE of the mean instead of SD of the mean (allowing to relate inferential statistical outcome to plotted curves; **please note that this does not allow to draw inferential conclusions on its own!!**)
 +  * Options visible (checkbox): if unchecked, all other controls are hidden and the axes is maximized to cover (almost) the entire figure (improved screenshots)
 +  * Baseline window (edit field): expression indicating the (relative-to-onsets) timepoints (in seconds!) that are used to compute the baseline for each extracted window (must be in Matlab'​s interval notation using three terms: ''​From:​Stepsize:​To''​ !), upon entering a new expression, the entire data will be recomputed, which can take a couple of seconds
 +  * Averaging window length (edit field): a single number indicating the length of the window being extracted (in seconds!)
 +  * virtual TR (edit field): a single number indicating the virtual resolution (in seconds!) of the visualization (allowing to improve response overlap for non-TR locked designs; very small numbers will increase the computational and plotting effort!)
 +  * Axes range X/Y from/to (edit fields): if the auto-scaling of the axes object is undesirable (e.g. to use the same scaling across several regions/​conditions/​studies/​etc.),​ the XLim and YLim axes properties can be set via these four edit controls; to revert to auto-scaling,​ simply enter an invalid number (e.g. any letter)
 +  * Error bands (checkbox): if checked, also visualize error band indicators (see also SE instead of SD setting above)
 +  * Individual response lines (checkbox, unlabeled): if checked, also plot individual responses (or within-subject averages for **RFX** setting; in the FFX case this can mean that **VERY** many lines are plotted, slowing down the UI!)
 +  * Background color setting (button): this button can be used to alter the background color of the axes
 +  * Error bands alpha setting (edit field): this number is used to set the alpha (transparency) property of the error bands
 +
 +===== Menu =====
 +The following functions are available via a menu:
 +
 +  * **File**
 +    * **Save extract datafile...** - stores the MDM/VOI content along with the extracted timecourses (and optionally created SDMs) and all settings to a ''​.MAT''​-file for later use (which then doesn'​t require any additional data, just NeuroElf for visualization!)
 +    * **Save figure screenshot...** - calls the private screenshot function of NeuroElf, requesting a filename, saving the figure as an image
 +    * **Save axes screenshot...** - moves the axes object to a new figure and then calls the private screenshot function of NeuroElf, requesting a filename, saving the axes object incl. the scale and title as an image
 +  * **Data**
 +    * **Set Data in Base Workspace** - make the data currently used available in the base workspace
 +  * **Options**
 +    * **Legend position** - allows to alter the position of the legend sub-axes to either of the four axes corners
 +    * **Subject selection** - brings up a listbox selector (''​listdlg''​) with the subject names, allows to exclude individual subjects from the plotter (e.g. to see if a particular subject is an outlier in all conditions, or otherwise shows an abnormal pattern)
 +
 +===== High-quality screenshot example =====
 +Using the File -> Save axes screenshot... menu item, it is possible to create high-quality plots by choosing the **Encapsulated PostScript (.eps)** format and then loading the EPS file into a graphics program (e.g. Adobe Photoshop or The GIMP). The above screenshot is then rendered (at any desired resolution),​ which will give nicer images for publication (please click on the image to zoom and compare!):
 +
 +{{:​neuroelf_gui:​mdm_voi_condavg_plot_hq.png?​600x400|High-quality image of the same plot using the screenshot functionality (click and zoom to compare...)}}
  
neuroelf_gui_-_mdm_voi_condition_average_ui.txt ยท Last modified: 2011/04/03 05:22 by jochen