neuroelf_gui_-_compute_multi-study_glm
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— | neuroelf_gui_-_compute_multi-study_glm [2011/04/03 05:25] (current) – created jochen | ||
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+ | ====== NeuroElf - compute multi-study GLM ====== | ||
+ | |||
+ | ===== Motivation ===== | ||
+ | While looking at the outcome of regressions on single runs (e.g. via using the [[vtc.CreateGLM|VTC:: | ||
+ | |||
+ | **This is currently the only menu-based and fully integrated way of performing full-volume-based time-course data regression in NeuroElf**, and it is implemented via the [[mdm.ComputeGLM|MDM:: | ||
+ | |||
+ | ===== Requirements ===== | ||
+ | Please read the [[mdm.ComputeGLM|page on GLM computation]] carefully before proceeding, so that you are aware of the options (not all of which are currently implemented in the GUI version, such as PPI settings, etc.). | ||
+ | |||
+ | ===== GUI layout ===== | ||
+ | {{: | ||
+ | |||
+ | ===== Controls ===== | ||
+ | The following controls are available: | ||
+ | |||
+ | * Base folder (edit field): This shows the location relative to which all file search operations are performed; **it is thus imperative to store the functional and design information data in a systematic way across subjects, using the same [[Processing stream - coding guidelines|coding rules]] and [[Processing stream - project folder structure|folder structure]] for each of them!** | ||
+ | * Base folder browse (button): Clicking on this button will bring up a folder selection dialog ('' | ||
+ | * VTC file pattern (edit field): file pattern identifying all VTC files to be found upon clicking the Find files button (see below) | ||
+ | * SDM/PRT file pattern (edit field): file pattern identifying all design specification files to be found upon clicking the Find files button | ||
+ | * Motion parameter files (checkbox): if checked, a click on the Find files button will also try to locate one motion parameters file per found VTC | ||
+ | * Motion parameter files (edit field, pattern): file pattern identifying the motion parameter files to be found upon clicking the Find files button (if and only if the preceding checkbox is ticked) | ||
+ | * + diff (checkbox): if checked (and motion parameter files are being used) also adds the first derivative of the motion parameters as confounds to the design matrix (see the [[mdm.ComputeGLM# | ||
+ | * + squared (checkbox): if checked (and motion parameter files are being used) also adds the squared (and mean-removed) motion parameters as confounds to the design matrix (see the [[mdm.ComputeGLM# | ||
+ | * Find files (button): **after entering and selecting the desired configuration of file names (patterns)**, | ||
+ | * List of VTC/ | ||
+ | * Add VTC+PRT/SDM (plus button): adds a single run's worth of data (single VTC and design specification file) to the list of files | ||
+ | * Remove selection (minus button): deletes the currently selected files from the lists | ||
+ | * Transformation (radio button group) with settings **none**, **PSC**, and **z**: | ||
+ | * **none** - no transformation is performed, timecourses are regressed "as is" | ||
+ | * **PSC** - %-change transformation (see [[psctrans]]) is performed prior to regression of the data | ||
+ | * **z** - z-transformation (see [[ztrans]]) is performed prior to regression of the data | ||
+ | * Intensity threshold (edit field): this value is passed as [[mdm.ComputeGLM# | ||
+ | * Mask file (dropdown): if opened and selected will bring up a file selector for a mask file | ||
+ | * Regression type (radio button group) with settings **OLS** and **robust**: | ||
+ | * **OLS** (Ordinary Least Squares): regression is performed under the single condition of minimizing the sum of squares of the residual using the normal equations where the residual term is orthogonal (sub-space) to the regressors (by simply matrix inversion and multiplication) | ||
+ | * **robust**: in principle comparable with **OLS** regression, but iteratively performs re-weighting of datapoints that, by the bisquare weighting function, are considered to be outliers (repeated up to 50 times, until weights converge on stable solution, see [[fitrobustbisquare_img]] and its default settings) | ||
+ | * Deconvolution (checkbox): if checked perform a deconvolution (see [[mdm.ComputeGLM# | ||
+ | * Nr. of lags (edit field): passed as [[mdm.ComputeGLM# | ||
+ | * Temp. filter (radio group) with settings **none**, **DCT**, and **Fourier**: | ||
+ | * **none**: no temporal filtering occurs (no addition to the design matrices) | ||
+ | * **DCT**: a set of DCT (discrete cosine transform) regressors is added to the design matrices | ||
+ | * **Fourier**: | ||
+ | * Cut-off (sec) (edit field): temporal filtering cut-off in seconds | ||
+ | * Global sigs (dropdown): **this control is not yet fully supported** only the numerical values (0, 1, or 2) are passed on as a number via the [[mdm.ComputeGLM# | ||
+ | * Target GLM file (edit field): filename for the resulting GLM file (if given, also sets the [[mdm.ComputeGLM# | ||
+ | * Specify (button): if clicked opens a file-saving dialog ('' | ||
+ | * Redo subjects (checkbox): if an existing filename is specified, the '' | ||
+ | * Load .mdm (button): brings up a file request dialog and loads the selected MDM file from disk | ||
+ | * Save .mdm (button): brings up a file-saving dialog and saves the MDM file (including the '' | ||
+ | * Show designs (checkbox): if checked shows the designs during computation (as plots) | ||
+ | * Cancel (button): closes the UI without further changes | ||
+ | * Compute VOIs... (button): **not yet functional, will use the [[mdm.ComputeVOIGLM|MDM:: | ||
+ | * Compute... (button): pass execution to the [[mdm.ComputeGLM|MDM:: | ||
neuroelf_gui_-_compute_multi-study_glm.txt · Last modified: 2011/04/03 05:25 by jochen