Differences

This shows you the differences between two versions of the page.

--- neuroelf_gui [2010/06/14 21:50] – reworked for full interface jochen
+++ neuroelf_gui [2011/05/07 22:44] – adapted panel view to newest version v0.9c jochen
@@ Line 24: / Line 24: @@
 Here is a full-resolution version with numbered areas which are explained below:
-{{:neuroelf_gui:main_ui_areas.png|NeuroElf Viewer (interface areas)}}
+{{:neuroelf_gui:main_ui_v09c_110507.png|NeuroElf GUI (full mode, panels)}}
 The numbered sections in turn mean:
   - dataset selection (among loaded objects)
   - statistical map selection (multi-select capable)
-  - configured clusters/regions of interest and output of cluster table (only for VMP/SMP format at this time)
+  - (a) configured clusters/regions of interest and (b) output of cluster table (only for HDR/HEAD/VMP format at this time) or beta extracts (only for RFX-GLM objects)
   - progress bar area (only visible if a long-running task is executed)
-  - dataset manipulation tools (only HDR/NII/VMR at this time)
+  - drawing tools (only HDR/NII/VMR at this time)
   - view (page) selection buttons and global transformation configuration
+  - contrast/brightness setting (button and slider axis)
   - cursor position in space (TAL/MNI coordinate and BV system coordinate, as well as volume selector)
   - configuration of statistical map (only VMP format at this time)
@@ Line 118: / Line 119: @@
   * minimize/maximize window
+==== Minimized mode ====
 Upon clicking this last, bottom-most button, the window will convert to minimized view (if it is in full mode, that is):
-{{:neuroelf_viewer_mini.png|NeuroElf Viewer (minimized)}}
+{{:neuroelf_gui:neuroelf_gui_minimized_v09c.png|NeuroElf GUI (minimized)}}
-The elements on the left side of the figure (file/map selector, cluster and table output) will be hidden from view to free up some space for other windows. The following 5 sections remain:
+The elements on the left side of the figure (file/map selector, cluster and table output) will be hidden from view to free up some space for other windows. The following sections remain:
   - sagittal view
   - coronal view
   - axial/transversal view
+  - drawing tools
+  - view/page selector
+  - contrast/brightness slider (and settings button)
   - current position
   - statistics configuration
+  - progress bar area
 ==== Cursor position in space ====
@@ Line 133: / Line 139: @@
 Additionally, for four-dimensional datasets, a volume selector and edit field allows to change the currently shown volume.
 ==== Configuration of statistical maps ====
 The first row of controls allows to set minimum and maximum thresholds for coloring the statistical map (any value below the minimum will not be shown, values above the maximum will be shown in the color of the maximum), and if the type and degrees of freedom of a statistical map is well-configured, one of the pre-defined probability threshold values can be selected as well (which automatically honors the number of tails selected below for one- or two-tailed statistical thresholding).
-In the second row, the positive and negative tails of the configured map can be en- and disabled separately, and also the cluster size threshold can be set and dis/enabled.
+In the second row, the positive and negative tails of the configured map can be en- and disabled separately, and also the cluster size threshold can be set and dis/enabled. **Note: whenever the cluster size thresholding is enabled, the values of the map will be set to zero for all non-clustered areas, which then is reflected in the ''Sampled values'' box!**
 The further controls are
@@ Line 194: / Line 199: @@
   * ''2'' key: toggle negative statistical tail on/off
-===== File menu =====
+===== Menus =====
-The ''File'' menu allows to load any xff-supported object, but only those displayable by the GUI will be added to the lists of selectable objects (FMR, HDR/NII, HEAD, SMP, SRF, VMP, VMR, VTC)
+For a list of menu items, please continue to the [[neuroelf_gui - menu tree|menu tree]] page.
-Additionally, any file loaded via the GUI will (if appropriate) be added to the list of recently loaded objects, so that in an upcoming session, formerly loaded files can be easily re-loaded.
-Under the ''Options'' submenu, the following entries are available:
-  * Stats colors (LUT)
-    * a list of files bundled with NeuroElf to alter the colortable for statistical maps
-  * Edit LUT palette - this calls up ''colorpicker'' for the currently selected LUT object
-  * Linked browsing -  if several voxel-views (at least one satellite figure with an anatomical dataset) is open, this will set the coordinate in all open windows upon clicking into any of those figures
-  * Echo function call/methods - if checked, this will cause NeuroElf GUI to print a line of code into the Matlab prompt window that can be used as a template for writing your own scripts
-===== Analysis menu =====
-Currently this menu has only one working entry:
-  * Contrast manager - this will bring up the [[NeuroElf - contrast manager|Contrast manager UI]]
-===== Visualization menu =====
-Currently this menu has only one entry:
-  * Create montage images - this will bring up the [[NeuroElf - montage UI|Image montage UI]]
-===== Tools menu =====
-The tools menu gives access to the following actions:
-  * SPM to BV conversion
-    * SPM.mat to PRT conversion ([[spmmat2prt.m]])
-    * SPM.mat to SDM conversion ([[spmmat2sdm]])
-  * [[alphasim]]
-  * [[renamedicom|Rename DICOM files]]
-  * [[spm5_preprojobs|SPM5/8 Preprocessing configuration]]
-  * [[tdclient]]
-  * Quality assessment
-    * [[fmriquality|fMRI quality assessment]]
-    * [[showspmrparams|Show SPM motion parameters]]