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plp.mkda [2011/08/24 18:50]
jochen added more info
plp.mkda [2011/08/24 19:47] (current)
jochen Added more info
Line 177: Line 177:
 ==== .contrasts ==== ==== .contrasts ====
-A cell array defining the contrasts for which coordinates will be selected (for positive and negative terms).+A cell array defining the contrasts for which coordinates will be selected (for positive and negative terms). ​Each cell must be a ''​1xC''​ double array containing at least one contrast identifier. Positive numbers refer to contrasts which will be used for as positive terms, negative numbers refer to contrasts which will be used as negative terms. E.g. the array ''​[1,​ -2]''​ would specify a contrast where the first and positive term is the contrast identified by ''​1''​ and the second and negative term is the contrast identified by ''​2''​. 
 +==== .grpmeth ==== 
 +This option sets the method used to compute the summary statistic. Possibly values are 
 +  * '''​ost'''​ - performs a one-sample t-test (highly experimental and not thoroughly tested!) 
 +  * '''​sum'''​ - computes the plain sum of the study-based maps 
 +  * '''​wsum'''​ - computes a weighted sum of the study-based maps; this is the default 
 +==== .indivmaps ==== 
 +This is a boolean flag (''​true''​ or ''​false''​) which defaults to ''​true''​. If set to true, the output VMP will contain one map per contrast and study representing the actual coordinates (which allows to inspect those maps for errors and further to visualize several maps at once for additional visualization options). 
 +==== .jbmeth ==== 
 +This option defines how the "​blobs"​ (kernel-filled spheres) are combined across coordinates,​ within study. If set to '''​max''',​ the maximum value will be used; if set to '''​rsum'''​ the sum is computed (but restricted to a maximum value of ''​1''​). This setting is experimental and the '''​max'''​ value should only be used in special cases and for testing. 
 +==== .pbar ==== 
 +An optional progress bar object, which then visualizes the progress across the Monte-Carlo simulations. 
 +==== .res ==== 
 +Resolution of the output VMP, default value is ''​3''​. Please note that **coordinates are sub-voxel exact computed** and that using higher resolutions (smaller values for this option) are only required if the data needs to be available in higher resolutions,​ e.g. for ROI generation, etc. 
 +==== .scale ===== 
 +This flag determines whether the kernel is interpreted as an indicator sphere ('''​indic'''​ setting) or as a gaussian kernel (which will be scaled to a maximum of ''​1'',​ '''​toone'''​ setting, which is the default). 
 +==== .smkern ==== 
 +Smoothing kernel(s). If multiple values are given, the MKDA analysis is performed for several kernels. The default is to use a single value of ''​8''​. 
 +==== .smkinterp ==== 
 +Smoothing kernel interpolation setting. Any value available for [[flexinterpn_method]] can be used. This determines what interpolation kernel will be used to determine the sub-voxel data. Given that the spatial frequency of the smoothing kernel is usually larger than twice the resolution, '''​linear'''​ is sufficient to prevent additional smoothing. 
 +==== .smkmdist ==== 
plp.mkda.txt · Last modified: 2011/08/24 19:47 by jochen