mdm.computeglm
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mdm.computeglm [2010/06/09 16:20] – created jochen | mdm.computeglm [2011/04/03 01:21] (current) – added individual explanation for options jochen | ||
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===== Motivation ===== | ===== Motivation ===== | ||
- | To combine several subjects' | + | To combine several subjects' |
This method then allows to perform the regression on a session-by-session basis and combine the results in one compound GLM object. | This method then allows to perform the regression on a session-by-session basis and combine the results in one compound GLM object. | ||
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This function is currently implemented for BrainVoyager QX's GLM format only. The following files must be available: | This function is currently implemented for BrainVoyager QX's GLM format only. The following files must be available: | ||
* VTC (or MTC) files for all runs of all subjects (e.g. the ones automatically created by spm5_preprojobs, | * VTC (or MTC) files for all runs of all subjects (e.g. the ones automatically created by spm5_preprojobs, | ||
- | * PRT (or the derived SDM) files for all runs (if subjects share this information, | + | * [[xff - PRT format|PRT]] |
- | * optionally the realignment parameter files (supported formats: TXT for SPM rp*.txt files, SDM for BV's motion correction output) | + | * optionally the realignment parameter files (supported formats: TXT for SPM rp*.txt files, |
**Note: The combination of within-subjects regressors (e.g. same condition across several runs) is done by identifying the subject ID as the particle of the time-course filename before the first underscore character!** This means that VTC (or MTC) filenames **must be named** as follows: | **Note: The combination of within-subjects regressors (e.g. same condition across several runs) is done by identifying the subject ID as the particle of the time-course filename before the first underscore character!** This means that VTC (or MTC) filenames **must be named** as follows: | ||
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| | ||
- | .globsigs | + | .globsigs |
+ | 0 - none | ||
+ | 1 - entire dataset (above threshold/ | ||
+ | 2 - two (one per hemisphere, split at BV Z=128) | ||
+ | 3 or more, perform PCA of time courses and first N | ||
+ | xff object(s), extract average time course from masks | ||
.ithresh | .ithresh | ||
.loadglm | .loadglm | ||
.mask optional masking, default: no mask (for now only VTC) | .mask optional masking, default: no mask (for now only VTC) | ||
.motpars | .motpars | ||
+ | .motparsd | ||
.motparsq | .motparsq | ||
.ndcreg | .ndcreg | ||
+ | .orthconf | ||
.outfile | .outfile | ||
.ppicond | .ppicond | ||
.ppirob | .ppirob | ||
| | ||
- | .ppivoi | + | .ppivoi |
+ | .ppivoiidx intra-VOI-object index (default: 1) | ||
.prtpnorm | .prtpnorm | ||
+ | .redo selected subjects will be overwritten (default: false) | ||
.regdiff | .regdiff | ||
.restcond | .restcond | ||
.robust | .robust | ||
+ | .savesdms | ||
+ | .showsdms | ||
+ | .shuflab | ||
+ | .shuflabm | ||
+ | .sngtrial | ||
+ | .sngtskip | ||
.subsel | .subsel | ||
.tfilter | .tfilter | ||
.tfilttype temporal filter type (either ' | .tfilttype temporal filter type (either ' | ||
+ | .transio | ||
.vweight | .vweight | ||
+ | .xconfound just as motpars, but without restriction on number | ||
| | ||
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| | ||
| | ||
- | for .ppi to work, the model filenames must be PRTs!</ | + | for .ppi to work, the model filenames must be PRTs! |
+ | all additional fields for the call to PRT:: | ||
+ | |||
+ | ===== Options ===== | ||
+ | |||
+ | ==== .globsigs ==== | ||
+ | Setting this field with either | ||
+ | * a number (other than 0) will add as many " | ||
+ | * a single VMR object or a cell array of VMR objects will add as many " | ||
+ | |||
+ | ==== .ithresh ==== | ||
+ | This field controls any explicit masking based on threshold (mean timecourse value). If left empty/ | ||
+ | |||
+ | ==== .loadglm ==== | ||
+ | If set to '' | ||
+ | |||
+ | ==== .mask ==== | ||
+ | Either a [[xff - MSK format|MSK object]] fitting the VTC spatial layout or a binary mask sufficing the same condition can be supplied to compute the GLM only within those voxels that are non zero/not false in the mask. | ||
+ | |||
+ | ==== .motpars ==== | ||
+ | If set to a cell array of filenames with size '' | ||
+ | |||
+ | ==== .motparsd ==== | ||
+ | If set to true any motion parameters will be added as is and their first derivative will also be part of the model. | ||
+ | |||
+ | ==== .motparsq ==== | ||
+ | If set to true any motion parameters will be added as is and their squared (and mean-removed) version will also be part of the model. | ||
+ | |||
+ | ==== .ndcreg ==== | ||
+ | If set to an integer number greater than 0, [[xff - PRT format|PRTs]] will be converted to design matrices using deconvolution designs (stick functions for each deconvolution/ | ||
+ | |||
+ | ==== .orthconf ==== | ||
+ | If set to true, confounds (motion parameters, filters, global timecourses, | ||
+ | |||
+ | ==== .outfile ==== | ||
+ | Can be set to a filename under which the GLM will be stored at the end of the computation (and, for robust regression and enabled transio after each subject). If '' | ||
+ | |||
+ | ==== .ppicond ==== | ||
+ | Can be set to a cell array with condition and/or contrast combinations, | ||
+ | * ''' | ||
+ | * ''' | ||
+ | * ''' | ||
+ | See also '' | ||
+ | |||
+ | ==== .ppirob ==== | ||
+ | **This option is experimental and not fully tested!** | ||
+ | |||
+ | Can be used to remove outliers of the PPI timecourse (which then improves RFX properties of beta estimates associated with the PPI regressors). | ||
+ | |||
+ | ==== .ppivoi ==== | ||
+ | Must be set to a valid [[xff - VOI format|VOI object]] for PPI to be used. | ||
+ | |||
+ | ==== .ppivoiidx ==== | ||
+ | Can be set to an index to select a specific VOI from the VOI object/file in option '' | ||
+ | |||
+ | ==== .prtpnorm ==== | ||
+ | If set to true, normalize and parameters in PRT files before computing the parametric conditional regressors (is passed as '' | ||
+ | |||
+ | ==== .redo ==== | ||
+ | If set to '' | ||
+ | |||
+ | ==== .regdiff ==== | ||
+ | **This option is experimental and not fully tested!** | ||
+ | |||
+ | If set to '' | ||
+ | |||
+ | ==== .restcond ==== | ||
+ | This option is passed as '' | ||
+ | |||
+ | ==== .robust ==== | ||
+ | If set to '' | ||
+ | |||
+ | ==== .savesdms ==== | ||
+ | Can be used to store created/ | ||
+ | |||
+ | ==== .showsdms ==== | ||
+ | If set to either ''' | ||
+ | |||
+ | ==== .shuflab ==== | ||
+ | **This option is experimental and not fully tested!** | ||
+ | |||
+ | Allows to re-generate the GLM under the null hypothesis of equal effect of stimuli across conditions by shuffling the labels (onsets across conditions). | ||
+ | |||
+ | ==== .shuflabm ==== | ||
+ | Sub-option for '' | ||
+ | |||
+ | ==== .sngtrial ==== | ||
+ | If set to '' | ||
+ | |||
+ | ==== .sngtskip ==== | ||
+ | Instructs the [[prt.ConvertToSingleTrial|PRT:: | ||
+ | |||
+ | ==== .subsel ==== | ||
+ | Cell array of subject IDs, sub-selects subjects from those referenced by the MDM file (see [[# | ||
+ | |||
+ | ==== .tfilter ==== | ||
+ | Sets the temporal filtering cutoff in seconds, so that filtering regressors will be added to the design matrix. | ||
+ | |||
+ | ==== .tfilttype ==== | ||
+ | Sets the temporal filtering type, one of ''' | ||
+ | |||
+ | ==== .transio ==== | ||
+ | If set to '' | ||
+ | |||
+ | ==== .vweight ==== | ||
+ | If set to '' | ||
+ | |||
+ | ==== .xconfound ==== | ||
+ | Can be set to a cell array with filenames of size '' | ||
===== Usage examples ===== | ===== Usage examples ===== | ||
Starting from scratch, the user has to do the following steps: | Starting from scratch, the user has to do the following steps: | ||
* locate the filenames of the VTC (or MTC and SSM/TSM) files to be regressed | * locate the filenames of the VTC (or MTC and SSM/TSM) files to be regressed | ||
- | * locate the filenames of the PRT (or SDM) files to be used as regressors (model) | + | * locate the filenames of the [[xff - PRT format|PRT]] |
* optionally locate the filenames of the realignment parameter files | * optionally locate the filenames of the realignment parameter files | ||
* make settings in the MDM structure | * make settings in the MDM structure |
mdm.computeglm.1276100404.txt.gz · Last modified: 2010/06/09 16:20 by jochen