Differences

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--- neuroelf_gui_-_menu_tree [2011/03/30 22:39] – created jochen
+++ neuroelf_gui_-_menu_tree [2011/04/14 21:30] – added vmr.CleanVMR and vmr.InhomogeneityCorrect items jochen
@@ Line 50: / Line 50: @@
   * **Border reconstruction** - the [[vmr.DBReco|VMR::DBReco]] method will be called on the currently selected VMR object, resulting in a [[xff - SRF format|SRF]] (surface) object that will subsequently be added to the NeuroElf GUI interface; this function is only useful if the currently selected VMR has been "segmented" (voxels above a certain threshold represent white matter voxels)!
-  * **Load Undo-Buffer...** - choosing this entry will ask the user to select a (secondary) VMR, which will be loaded and its data stored in the currently selected VMR's ''RunTimeVars.UndoBuffer'' property, allowing to draw data from a different object into the currently selected VMR's data (using the "undo-drawing" functionality)
+  * **Clean VMR** - call the [[vmr.CleanVMR|VMR::CleanVMR]] method to create a second (copy) of the VMR with all voxels detected as background set to 0
+  * **Correct inhomogeneity** - call the [[vmr.InhomogeneityCorrect|VMR::InhomogeneityCorrect]] method, which in turn uses the [[pmbfilter]] function in 3 passes to auto-correct the inhomogeneity of the data
   * **Smooth VMR** - this opens up a small dialog box, where smoothing kernel, bounding box, as well as an optional value range can be specified; subsequently the [[aft.SmoothData3D|AFT::SmoothData3D]] method will be called to perform the data smoothing (for now, this may require a large amount of memory, depending on the settings; this might lead to out-of-memory error conditions, particularly for 0.5mm-resolution VMRs!)
+  * **Load Undo-Buffer...** - choosing this entry will ask the user to select a (secondary) VMR, which will be loaded and its data stored in the currently selected VMR's ''RunTimeVars.UndoBuffer'' property, allowing to draw data from a different object into the currently selected VMR's data (using the "undo-drawing" functionality)
 ===== VTC menu =====
@@ Line 105: / Line 107: @@
   * **alphasim...** - if the currently selected (voxel-based) statistical object is a VMP, this will first create a mask from all non-zero voxels of the currently selected map(s) and then request the user to enter a number of iterations, after which the ''alphasim'' function is called and results are being reported in the Matlab console window
   * **Rename DICOM files...** - this will call [[renamedicom]] without any parameters, which will open its own UI
-  * **SPM5 preprocessing...** - this will open the UI of [[spm5_prepro]], a function that configures a standardized SPM5/SPM8-based stream of preprocessing steps
+  * **SPM5 preprocessing...** - this will open the UI of [[spm5_preprojobs]], a function that configures a standardized SPM5/SPM8-based stream of preprocessing steps
   * **tdclient...** - this opens up the [[neuroelf_gui - tdclient UI]]
   * **Quality assessment** - this is a sub-item menu with ...