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neuroelf_gui_-_compute_multi-study_glm [2011/04/03 07:25] (current)
jochen created
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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::​CreateGLM]] and [[glm.SingleStudy_tMap|GLM::​SingleStudy_tMap]] methods) can already be instructive,​ most neuroimaging studies focus on trying to draw conclusions that can be generalized to the entirety of subject population (where the participants in the actual study represent a randomly drawn sample, and one candidate for an appropriate statistical test thus is a random-effects t-map).
 +**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::​ComputeGLM]] method. To simplify file selection, NeuroElf comes with its own UI for this task.
 +===== 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 =====
 +{{:​neuroelf_gui:​mdm_compute_glm_dialog.png|Multi-study GLM computation dialog (using the MDM::​ComputeGLM method)}}
 +===== 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 (''​uigetdir''​),​ and upon successfully selecting a folder, the Base folder edit field will be set to the selected folder location
 +  * 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#​motparsd|.motparsd]] flag)
 +  * + 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#​motparsd|.motparsq]] flag)
 +  * Find files (button): **after entering and selecting the desired configuration of file names (patterns)**,​ clicking this button will use two (or three) calls to [[findfiles]] to locate the VTC and PRT (as well as motion parameter) files for the current analysis; **if the number and/or names of folders containing the files mismatch, an error message is given**, otherwise the filenames are shown in the listboxes underneath
 +  * List of VTC/​design/​motion parameter files (multi-selection listboxes): "​linked"​ listboxes (selection of files in one listbox will also set the same selection in the other (two) enabled listbox)
 +  * 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#​ithresh|.ithresh]] flag
 +  * 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#​ndcregs|.ndcregs]] flag)
 +  * Nr. of lags (edit field): passed as [[mdm.ComputeGLM#​ndcregs|.ndcregs]] flag **if and only if** the previous checkbox is ticked (otherwise this flag is set to 0)
 +  * 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**:​ a Fourier basis set up to a certain frequency is added to the design matrices
 +  * 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#​globsigs|.globsigs]] flag
 +  * Target GLM file (edit field): filename for the resulting GLM file (if given, also sets the [[mdm.ComputeGLM#​loadglm|.loadglm]] flag to ''​true''​)
 +  * Specify (button): if clicked opens a file-saving dialog (''​uiputfile''​) and fills the Target GLM file edit field
 +  * Redo subjects (checkbox): if an existing filename is specified, the ''​.loadglm''​ flag will be set to ''​true''​ (see above), and the user can then choose whether or not to only "​add"​ new subject or to redo all subjects referenced in the current MDM selection
 +  * 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 ''​.RunTimeVars''​ settings) to disk
 +  * 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::​ComputeVOIGLM]] method equivalently,​ dialog is missing a VOI selection tool!**
 +  * Compute... (button): pass execution to the [[mdm.ComputeGLM|MDM::​ComputeGLM]] method, opens the resulting GLM, and then closes the UI
neuroelf_gui_-_compute_multi-study_glm.txt ยท Last modified: 2011/04/03 07:25 by jochen