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vmp.clustertable [2010/07/04 17:16]
jochen created
vmp.clustertable [2014/06/04 19:57] (current)
jochen updated method
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-====== ​vmp.ClusterTable ======+====== ​obj.ClusterTable ======
  
 ===== Motivation ===== ===== Motivation =====
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   * looking up the closest Talairach label for each peak coordinate (using a toolbox-builtin local TD database function)   * looking up the closest Talairach label for each peak coordinate (using a toolbox-builtin local TD database function)
  
-===== Method reference ('vmp.Help('​ClusterTable'​)'​) ===== +===== Method reference ('obj.Help('​ClusterTable'​)'​) ===== 
-<​file> ​VMP::​ClusterTable ​ - generate a table with clusters+<​file> ​OBJ::​ClusterTable ​ - generate a table with clusters
    
- ​FORMAT: ​      [c, t, v, vo] = vmp.ClusterTable(mapno [, thresh [, opts]])+ ​FORMAT: ​      [c, t, v, vo] = obj.ClusterTable(mapno [, thresh [, opts]])
    
  Input fields:  Input fields:
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        ​opts ​       optional settings        ​opts ​       optional settings
         .altmaps ​  ​alternative maps to extract values from (default: [])         .altmaps ​  ​alternative maps to extract values from (default: [])
 +        .altstat ​  ​either of '​mean'​ or {'​peak'​}
         .cclag ​    flag, interpret the threshold as lag number (false)         .cclag ​    flag, interpret the threshold as lag number (false)
         .clconn ​   cluster connectivity ('​face',​ {'​edge'​},​ '​vertex'​)         .clconn ​   cluster connectivity ('​face',​ {'​edge'​},​ '​vertex'​)
 +        .icbm2tal ​ flag, VMP coords are passed to icbm2tal (default: false)
         .localmax ​ break down larger clusters threshold (default: Inf)         .localmax ​ break down larger clusters threshold (default: Inf)
 +        .localmaxi iterate on sub-clusters (default: false)
         .localmin ​ minimum size for sub-clusters (default: 2)         .localmin ​ minimum size for sub-clusters (default: 2)
 +        .localmsz ​ print sub-cluster sizes (default: false)
 +        .lupcrd ​   look-up coordinate, either or '​center',​ '​cog',​ {'​peak'​}
         .minsize ​  ​minimum cluster size (map resolution, default by map)         .minsize ​  ​minimum cluster size (map resolution, default by map)
         .mni2tal ​  flag, VMP coords are passed to mni2tal (default: false)         .mni2tal ​  flag, VMP coords are passed to mni2tal (default: false)
         .showneg ​  flag, negative values are considered (default: false)         .showneg ​  flag, negative values are considered (default: false)
         .showpos ​  flag, positive values are considered (default: true)         .showpos ​  flag, positive values are considered (default: true)
-        .sorting ​  ​either of {'​maxstat'​},​ '​size',​ '​x',​ '​y',​ '​z'​+        .sorting ​  ​either of '​maxstat', {'​maxstats'}, '​size',​ '​x',​ '​y',​ '​z'​ 
 +        .svc       ​small-volume correction (either VOI, voxels, or image) 
 +        .svcthresh threshold for SVC (default: 0.05)
         .tdclient ​ flag, lookup closest talairach label (default false)         .tdclient ​ flag, lookup closest talairach label (default false)
    
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        ​v ​          ​thresholded map (in VMP resolution!)        ​v ​          ​thresholded map (in VMP resolution!)
        ​vo ​         if requested, VOI structure with (TAL) coords        ​vo ​         if requested, VOI structure with (TAL) coords
 + 
 + ​TYPES:​ CMP, HDR, HEAD, MSK, VMP
    
  Note: if only one output is requested, the table is text table is  Note: if only one output is requested, the table is text table is
-       ​returned!!</​file>​+       ​returned!! 
 +  
 + Note: icbm2tal overrides mni2tal! 
 +  
 + Note: svc only valid for VMP (given FWHM estimate in RunTimeVars!)</​file>​
  
 ===== Arguments ===== ===== Arguments =====
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 === .altmaps === === .altmaps ===
 Lists the indices of maps to extract statistical values at the coordinates of the peaks in the selected map (''​mapno''​ argument). Lists the indices of maps to extract statistical values at the coordinates of the peaks in the selected map (''​mapno''​ argument).
 +
 +=== .altstat ===
 +Selects whether the peak or the mean for the additional maps is extracted and shown.
  
 === .cclag === === .cclag ===
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 === .clconn === === .clconn ===
 Overrides the default for the setting as how to determine whether two adjacent voxels are connected (belong to the same cluster); whereas '''​face'''​ means that voxels must be direct neighbors (coordinate value may only be different by 1 voxel in one dimension), '''​edge'''​ (which is the default) means that voxels are also considered to be connected when the coordinate values differ by up to 1 in two dimensions, and '''​vertex'''​ finally means that voxels which are only connected by one of their vertices (full spatial diagonal where all dimensions differ by 1 in either direction) are considered to be part of one cluster. Overrides the default for the setting as how to determine whether two adjacent voxels are connected (belong to the same cluster); whereas '''​face'''​ means that voxels must be direct neighbors (coordinate value may only be different by 1 voxel in one dimension), '''​edge'''​ (which is the default) means that voxels are also considered to be connected when the coordinate values differ by up to 1 in two dimensions, and '''​vertex'''​ finally means that voxels which are only connected by one of their vertices (full spatial diagonal where all dimensions differ by 1 in either direction) are considered to be part of one cluster.
 +
 +=== .icbm2tal ===
 +Turns on ICBM2TAL conversion (using the [[icbm2tal]] function) **for the text output (only)** instead of mni2tal.
  
 === .localmax === === .localmax ===
 Sets a threshold (related to cluster size in number of voxels) for which an attempt is made to search for local maxima (or minima for negative values) within the given cluster. The default is ''​Inf''​ which means that clusters are not being searched for local maxima. Sets a threshold (related to cluster size in number of voxels) for which an attempt is made to search for local maxima (or minima for negative values) within the given cluster. The default is ''​Inf''​ which means that clusters are not being searched for local maxima.
 +
 +=== .localmaxi ===
 +Flag to turn on iterating over sub-clusters until no more splitting can be performed.
  
 === .localmin === === .localmin ===
 Sets the minimal size of sub-clusters (useful restriction for maps that have been masked, where the local maxima might be at the very edge of the cluster; please see [[splitclustercoords]] for more information). Sets the minimal size of sub-clusters (useful restriction for maps that have been masked, where the local maxima might be at the very edge of the cluster; please see [[splitclustercoords]] for more information).
 +
 +=== .localmsz ===
 +Flag whether or not to print sub-cluster sizes (in text output).
 +
 +=== .lupcrd ===
 +Which coordinate to print in the text output (center, i.e. mean, center-of-gravity,​ i.e. the stats-weighted mean, or peak).
  
 === .minsize === === .minsize ===
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 === .sorting === === .sorting ===
 Alters the way in which clusters are sorted for both table and [[xff - VOI format|VOI]] outputs. The default value, '''​maxstat'''​ means that clusters with a higher (absolute) statistical value will appear before clusters with a lower statistical value in the output. The value '''​size'''​ sorts from larger to smaller clusters, and the values '''​x''',​ '''​y''',​ and '''​z'''​ will sort clusters by their coordinate (in the given dimension). Alters the way in which clusters are sorted for both table and [[xff - VOI format|VOI]] outputs. The default value, '''​maxstat'''​ means that clusters with a higher (absolute) statistical value will appear before clusters with a lower statistical value in the output. The value '''​size'''​ sorts from larger to smaller clusters, and the values '''​x''',​ '''​y''',​ and '''​z'''​ will sort clusters by their coordinate (in the given dimension).
 +
 +=== .svc ===
 +If a small-volume is provided in this field (either a VOI object, an image object, or a list of coordinates),​ perform SVC on the selected map (only works for VMP maps, and creates a new map in the object).
 +
 +=== .svcthresh ===
 +Corrected threshold for SVC.
  
 === .tdclient === === .tdclient ===
vmp.clustertable.txt · Last modified: 2014/06/04 19:57 by jochen