neuroelf_gui_-_glm_beta_plotter
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neuroelf_gui_-_glm_beta_plotter [2011/05/07 23:13] – added screenshot of beta plotter with scatter plot and quadratic fit jochen | neuroelf_gui_-_glm_beta_plotter [2011/05/18 13:25] (current) – changing vertical resolution to 204 to include bar jochen | ||
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===== Motivation ===== | ===== Motivation ===== | ||
- | This tool is mostly meant as a quick visualization for the assessment of whether or not a statistical test value (t-contrast) found in a specific part of the brain "makes sense" w.r.t. the hypothesis of the study. | + | This tool is mostly meant as a quick visualization for the assessment of whether or not a statistical test value (t-contrast) found in a specific part of the brain "makes sense" w.r.t. the hypothesis of the study, and in part also to identify outlier subjects. |
For instance, if the design contains two sets of stimuli (images and temperatures, | For instance, if the design contains two sets of stimuli (images and temperatures, | ||
===== Requirements ===== | ===== Requirements ===== | ||
- | A GLM file must be loaded and selected as the currently used statistics object, which will then enable the user to use the [[NeuroElf GUI - menu tree# | + | A RFX-GLM file must be loaded and selected as the currently used statistics object, which will then enable the user to use the [[NeuroElf GUI - menu tree# |
===== Opening the UI ===== | ===== Opening the UI ===== | ||
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===== GUI layout ===== | ===== GUI layout ===== | ||
+ | {{ youtube> | ||
+ | When initially opening the beta plotter, the bar graph option will be selected (watch the video on the GLM beta plotter on the right, or go to the [[NeuroElf GUI - GLM beta plotter video|full resolution]] page): | ||
+ | |||
{{: | {{: | ||
+ | |||
+ | The following screenshot shows a different dataset, where a covariate (age) was scattered against a contrast, and a quadratic fit was computed: | ||
+ | |||
{{: | {{: | ||
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The following controls are available: | The following controls are available: | ||
- | * Plot type (dropdown) with settings **Bar graph**, **Scatter plot**, **Scatter plot + OLS**, and **Scatter plot + robust** | + | * Plot type (dropdown) with settings **Bar graph**, **Scatter plot** |
- | * when **Bar graph** is selected, the average (and optional individual) beta or contrast values will be shown as bars (and on-top-of-bar scatter points), with optional error bars | + | * when **Bar graph** is selected, the average (and optional individual) beta or contrast values will be shown as bars (and on-top-of-bar scatter points), with optional error bars, subject labels (if points are plotted) and trend lines (if more than one bar per group is shown) |
* when **Scatter plot** is selected (only available when a covariate is configured and selected as well), the beta or contrast values of the first selected predictor/ | * when **Scatter plot** is selected (only available when a covariate is configured and selected as well), the beta or contrast values of the first selected predictor/ | ||
- | * when **Scatter plot + OLS** is selected, an additional regression line will be drawn | ||
- | * when **Scatter plot + robust** is selected, the additionally drawn regression line represents the outcome of a robust regression | ||
* Update (checkbox): if checked, the plot updates with the cursor position and also when a cluster is selected from the list of VOIs | * Update (checkbox): if checked, the plot updates with the cursor position and also when a cluster is selected from the list of VOIs | ||
* Radius (edit field): when the brain is browsed with the Update box checked, this determines the sampling size for the displayed betas (default being 0, meaning that only one voxel worth of data is shown) | * Radius (edit field): when the brain is browsed with the Update box checked, this determines the sampling size for the displayed betas (default being 0, meaning that only one voxel worth of data is shown) | ||
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* Select contrasts (multi-selection listbox): same as conditions, selecting one or more contrasts de-selects all conditions | * Select contrasts (multi-selection listbox): same as conditions, selecting one or more contrasts de-selects all conditions | ||
* Contrast color settings (button): same as condition colors | * Contrast color settings (button): same as condition colors | ||
- | * Select covariate (single-selection listbox): only used when Plot type is set to one of the **Scatter plot** | + | * Select covariate (single-selection listbox): only used when Plot type is set to the **Scatter plot** |
- | * Enable groups (checkbox): if groups are configured in the GLM file (see [[NeuroElf GUI - contrast manager|Contrast manager UI]]), bar graphs | + | * Enable groups (checkbox): if groups are configured in the GLM file (see [[NeuroElf GUI - contrast manager|Contrast manager UI]]), bar graphs |
- | * Groups (multi-selection listbox): if groups are enabled (checkbox ticked), and the Plot type is set to **Bar graph**, bars and beta/ | + | * Groups (multi-selection listbox): if groups are enabled (checkbox ticked), bars and scatters of (mean) |
* Options visible (checkbox): if unchecked, all other controls are hidden and the axes is maximized to cover (almost) the entire figure (improved screenshots) | * Options visible (checkbox): if unchecked, all other controls are hidden and the axes is maximized to cover (almost) the entire figure (improved screenshots) | ||
* 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/ | * 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/ | ||
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* **Data** | * **Data** | ||
* **Set Data in Base Workspace** - make the data currently used available in the base workspace | * **Set Data in Base Workspace** - make the data currently used available in the base workspace | ||
+ | * **Copy plot to separate figure** - copies the plot with its current configuration into a separate figure (which is useful for annotations, | ||
* **Options** | * **Options** | ||
+ | * **Legend settings** - sub-menu with items | ||
+ | * **Legend for bars** - if selected (and subsequently being " | ||
+ | * **Legend for scatters** - if selected (and subsequently being " | ||
+ | * **Legend position** - a sub-section with entries **Northwest** (default), **Northeast**, | ||
+ | * **Remove zero (0) values** - if selected (and subsequently being " | ||
+ | * **Robust stats** - if selected (and subsequently being " | ||
+ | * **Scatter options** - sub-section with entries | ||
+ | * **apply groups separately** - if selected (and subsequently being " | ||
+ | * **best-fit straight line** - if selected (and subsequently being " | ||
+ | * **best-fit quadratic** - if selected (and subsequently being " | ||
+ | * **confidence ellipse** - if selected (and subsequently being " | ||
+ | * **set marker type** - sub-menu with items for circle (** o **), cross (** x **), plus (** + **), asterisk (** * **), dot (** . **), square (**square**), | ||
+ | * **statistics output** - if selected (and subsequently being " | ||
+ | * **use filled markers** - if selected (and subsequently being " | ||
+ | * **Subject labels** - if selected (and subsequently being " | ||
+ | * **Subject profile lines** - if selected (and subsequently being " | ||
* **Subject selection** - brings up a listbox selector ('' | * **Subject selection** - brings up a listbox selector ('' | ||
+ | ===== High-quality output ===== | ||
+ | Using the **File -> Save full axes screenshot...** feature, and subsequently selecting EPS as format (and rasterizing the resulting file in either Photoshop or The GIMP), you can create high-quality images of the beta plotter: | ||
+ | |||
+ | {{: |
neuroelf_gui_-_glm_beta_plotter.1304810018.txt.gz · Last modified: 2011/05/07 23:13 by jochen