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mdm.computeglm [2010/06/16 17:18] – changed PRT and SDM texts to links to their file format pages jochenmdm.computeglm [2010/11/24 05:13] – updated the help jochen
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        options     optional 1x1 struct with fields        options     optional 1x1 struct with fields
-        .globsigs  add C components (of slices) as confounds (default: 0)+        .globsigs  add global signals as confound, one of 
 +                   0 - none 
 +                   1 - entire dataset (above threshold/within mask) 
 +                   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   intensity threshold, default: 100         .ithresh   intensity threshold, default: 100
         .loadglm   boolean flag, load GLM file named in .outfile         .loadglm   boolean flag, load GLM file named in .outfile
         .mask      optional masking, default: no mask (for now only VTC)         .mask      optional masking, default: no mask (for now only VTC)
         .motpars   motion parameters (Sx1 cell array with sdm/txt files)         .motpars   motion parameters (Sx1 cell array with sdm/txt files)
 +        .motparsd  also add diff of motion parameters (default: false)
         .motparsq  also add squared motion parameters (default: false)         .motparsq  also add squared motion parameters (default: false)
         .ndcreg    if set > 0, perform deconvolution (only with PRTs!)         .ndcreg    if set > 0, perform deconvolution (only with PRTs!)
 +        .orthconf  orthogonalize confounds (and motion parameters, true)
         .outfile   output filename of GLM file, default: no saving         .outfile   output filename of GLM file, default: no saving
         .ppicond   list of regressors (or differences) to interact         .ppicond   list of regressors (or differences) to interact
         .ppirob    perform robust regression on VOI timecourse and remove         .ppirob    perform robust regression on VOI timecourse and remove
                    outliers from timecourse/model (threshold, default: 0)                    outliers from timecourse/model (threshold, default: 0)
-        .ppivoi    VOI used to extract time-course from+        .ppivoi    VOI object used to extract time-course from 
 +        .ppivoiidx intra-VOI-object index (default: 1)
         .prtpnorm  normalize parameters of PRT.Conds (true)         .prtpnorm  normalize parameters of PRT.Conds (true)
 +        .redo      selected subjects will be overwritten (default: false)
         .regdiff   flag, regress first discreet derivatives (diff) instead         .regdiff   flag, regress first discreet derivatives (diff) instead
         .restcond  remove rest condition (rest cond. name, default: '')         .restcond  remove rest condition (rest cond. name, default: '')
         .robust    perform robust instead of OLS regression         .robust    perform robust instead of OLS regression
 +        .savesdms  token, if not empty, save on-the-fly SDMs (e.g. '.sdm')
 +        .showsdms  token, passed to SDM::ShowDesign (if valid)
 +        .shuflab   PRT labels (conditions names) to shuffle
 +        .shuflabm  minimum number of onsets per label (1x1 or 1xL)
         .subsel    cell array with subject IDs to work on         .subsel    cell array with subject IDs to work on
         .tfilter   add filter regressors to SDMs (cut-off in secs)         .tfilter   add filter regressors to SDMs (cut-off in secs)
         .tfilttype temporal filter type (either 'dct' or {'fourier'})         .tfilttype temporal filter type (either 'dct' or {'fourier'})
         .vweight   combine runs/studies variance-weighted (default: false)         .vweight   combine runs/studies variance-weighted (default: false)
 +        .xconfound just as motpars, but without restriction on number
    
  Output fields:  Output fields:
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        regression models (to allow later continuation of crashed/broken        regression models (to allow later continuation of crashed/broken
        computation using the .subsel field)        computation using the .subsel field)
-       for .ppi to work, the model filenames must be PRTs!</file>+       for .ppi to work, the model filenames must be PRTs! 
 +       all additional fields for the call to PRT::CreateSDM are supported!</file>
  
 ===== Usage examples ===== ===== Usage examples =====
mdm.computeglm.txt · Last modified: 2011/04/03 01:21 by jochen