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neuroelf_gui [2011/05/07 22:44] – adapted panel view to newest version v0.9c jochenneuroelf_gui [2011/05/18 13:23] (current) – changing vertical resolution to 204 to include bar jochen
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 ===== GUI layout ===== ===== GUI layout =====
 +{{ youtube>pMY6fvv-Sj4?320x204| NeuroElf - basic browsing}}
 The GUI comes in two modes, full and minimized (whereas minimized removes some UI elements from the figure so as to save some space for other windows). The GUI comes in two modes, full and minimized (whereas minimized removes some UI elements from the figure so as to save some space for other windows).
 +\\
 +\\
 +\\
 +\\
 +\\
  
 To bring up the GUI, simply issue the To bring up the GUI, simply issue the
 +\\
  
 <code matlab>% bring up NeuroElf GUI <code matlab>% bring up NeuroElf GUI
 neuroelf_gui</code> neuroelf_gui</code>
 +\\
  
-call. It will take a couple of seconds (especially if the xfigure class needs to be run-time compiled by Matlab on its first call), after which the following UI figure will appear:+call. It will take a couple of seconds (especially if the xfigure class needs to be run-time compiled by Matlab on its first call), after which the following UI figure will appear (watch the video on the right hand side, also available in [[NeuroElf basic browsing|full resolution]]):
  
-{{:neuroelf_gui:main_ui_empty.png?640|NeuroElf Viewer (full mode, no stats)}}+{{:neuroelf_gui:main_ui_empty_v09c_110512.png?640|NeuroElf Viewer (full mode, no stats)}}
  
-After loading or creating some statistical map (and, in this case, the Colin brain VMR), the display has more buttons un-grayed:+After creating some additional files (see [[neuroelf_makefiles]] for more instructions), loading or creating some statistical map (and, in this case, the newly created Colin brain VMR) and using the Clustertable functionality, the display has more buttons un-grayed:
  
-{{:neuroelf_gui:main_ui.png?640|NeuroElf Viewer (full mode with stats)}}+{{:neuroelf_gui:main_ui_v09c_110512.png?640|NeuroElf GUI (full mode with stats)}}
  
 Here is a full-resolution version with numbered areas which are explained below: Here is a full-resolution version with numbered areas which are explained below:
  
-{{:neuroelf_gui:main_ui_v09c_110507.png|NeuroElf GUI (full mode, panels)}}+{{:neuroelf_gui:main_ui_panels_v09c_110512.png|NeuroElf GUI (full mode, panels)}}
  
 The numbered sections in turn mean: The numbered sections in turn mean:
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     * c) axial/transversal view     * c) axial/transversal view
  
-==== Dataset selection ====+==== Dataset selection (1) ====
 The dropdown controls allow to select any of the loaded datasets as the currently active dataset (both for anatomical and statistical datasets). Currently supported are The dropdown controls allow to select any of the loaded datasets as the currently active dataset (both for anatomical and statistical datasets). Currently supported are
   * as anatomical datasets   * as anatomical datasets
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     * HDR/NII (Analyze/NIftI format, incl. 4D NIftI files)     * HDR/NII (Analyze/NIftI format, incl. 4D NIftI files)
     * HEAD (AFNI's BRIK/HEAD format, anatomical auto-detect)     * HEAD (AFNI's BRIK/HEAD format, anatomical auto-detect)
 +    * MSK (BrainVoyager's Mask format)
     * VMR (BrainVoyager's Volumetric MR format)     * VMR (BrainVoyager's Volumetric MR format)
     * VTC (BrainVoyager's Volumetric TimeCourse format)     * VTC (BrainVoyager's Volumetric TimeCourse format)
   * as statistical datasets   * as statistical datasets
 +    * CMP (BrainVoyager's Component Map format)
     * GLM (BrainVoyager's General Linear Model format)     * GLM (BrainVoyager's General Linear Model format)
 +    * HDR/NII (Analyze/NIftI format, requires special tokens in description or settings in ''RunTimeVars'')
     * HEAD (AFNI's BRIK/HEAD format, statistical auto-detect)     * HEAD (AFNI's BRIK/HEAD format, statistical auto-detect)
     * VMP (BrainVoyager's Volumentic Map format)     * VMP (BrainVoyager's Volumentic Map format)
- 
-Please note: Statistical maps from SPM must currently be imported into BrainVoyager's VMP format for thresholded map display! 
  
 In addition to the selection, for each dataset a transformation quaternion (origin) can be set separately, in case datasets from different programs are not initially compatible (3D transformation button). Once a dataset is no longer required in the list, it can be removed from the dropdown (using the x-button). In addition to the selection, for each dataset a transformation quaternion (origin) can be set separately, in case datasets from different programs are not initially compatible (3D transformation button). Once a dataset is no longer required in the list, it can be removed from the dropdown (using the x-button).
  
-==== Statistical map selection ====+==== Statistical map selection (2) ====
 Once an object is loaded suitable for statistical map overlay, the maps therein can be displayed, also supporting a multi-selection of maps. Additionally, the following actions are supported: Once an object is loaded suitable for statistical map overlay, the maps therein can be displayed, also supporting a multi-selection of maps. Additionally, the following actions are supported:
   * moving maps within their container (HEAD and VMP format, arrow up and down buttons)   * moving maps within their container (HEAD and VMP format, arrow up and down buttons)
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   * deleting maps from their container (HEAD and VMP format, trashcan button)   * deleting maps from their container (HEAD and VMP format, trashcan button)
   * computing a formula on the available map data (VMP format only, //f//-button, see [[vmp.ComputeFormula]] for more info)   * computing a formula on the available map data (VMP format only, //f//-button, see [[vmp.ComputeFormula]] for more info)
 +  * sampling the selected maps as surface maps (SMP) for the currently visible surfaces (SRF objects selected in Scenery listbox)
   * propagating the map condition selection for other subjects (GLM format, ellipse-button)   * propagating the map condition selection for other subjects (GLM format, ellipse-button)
  
-==== Configured clusters and table output ====+==== Configured clusters and table output (3a/3b) ====
 Below the map area is the listbox that contains the currently configured clusters (comparable to BrainVoyager's ROI dialog). Each time the Clustertable button in the stats area is used, the clusters will be overwritten, so **make sure to save any desired/altered list of clusters** before using the Clustertable function again! Below the map area is the listbox that contains the currently configured clusters (comparable to BrainVoyager's ROI dialog). Each time the Clustertable button in the stats area is used, the clusters will be overwritten, so **make sure to save any desired/altered list of clusters** before using the Clustertable function again!
  
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   * a table of extracted betas (also showing each subject's name and the label of the cluster from which the data was drawn)   * a table of extracted betas (also showing each subject's name and the label of the cluster from which the data was drawn)
  
-==== Progress bar ====+==== Progress bar (4) ====
 For some longer-running tasks (e.g. alphasim or robust regression of contrasts), a progress bar is shown and updated regularly. This allows the UI to remain mostly function (browsing, shorter tasks) while a longer task is completing in the back-ground. For some longer-running tasks (e.g. alphasim or robust regression of contrasts), a progress bar is shown and updated regularly. This allows the UI to remain mostly function (browsing, shorter tasks) while a longer task is completing in the back-ground.
  
-==== Dataset manipulation buttons ====+==== Dataset manipulation buttons (5) ====
 From top to bottom, these buttons are associated with the following actions/settings: From top to bottom, these buttons are associated with the following actions/settings:
   * browsing mode (drawing disabled)   * browsing mode (drawing disabled)
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   * floodfill (3D flood-filling of voxels that match the selected criteria)   * floodfill (3D flood-filling of voxels that match the selected criteria)
   * marker expansion (expanding the marked selection in a dilation fassion)   * marker expansion (expanding the marked selection in a dilation fassion)
 +  * smoothing of the gray-scale data (allowing a coordinate and value range selection, as well as setting a smoothing kernel)
   * smoothing (the marked selection is smoothed to remove rough edges)   * smoothing (the marked selection is smoothed to remove rough edges)
   * undo drawing en/disable (drawing takes back values from the buffer)   * undo drawing en/disable (drawing takes back values from the buffer)
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   * reload marked (reload dataset from disk and mask with marked color)   * reload marked (reload dataset from disk and mask with marked color)
   * reload unmarked (reload dataset from disk and inverse-mask with marked color)   * reload unmarked (reload dataset from disk and inverse-mask with marked color)
 +  * defining a new ROI (cluster) to be added to the list of clusters (VOI list)
 +  * setting the underlay object
  
-==== View / Page selection ====+==== View / Page selection (6) ====
 The main UI has three different views: The main UI has three different views:
  
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 The view/page selection buttons, from top to bottom, mean: The view/page selection buttons, from top to bottom, mean:
   * undocking (create a secondary, satellite figure containing the current view, allowing to investigate multiple maps/datasets, potentially at the same coordinate via linked browsing)   * undocking (create a secondary, satellite figure containing the current view, allowing to investigate multiple maps/datasets, potentially at the same coordinate via linked browsing)
 +  * toggle between linked and linked browsing (state obversable)
 +  * minimize/maximize window
   * switch to three-slice view (page 1, default on startup)   * switch to three-slice view (page 1, default on startup)
   * switch to sagittal-zoomed view (page 2, SAG)   * switch to sagittal-zoomed view (page 2, SAG)
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   * set global spatial transformation parameters (in case data comes from a different program)   * set global spatial transformation parameters (in case data comes from a different program)
   * switch to surface rendering view (page 3)   * switch to surface rendering view (page 3)
-  * minimize/maximize window+  * invoke voxel-based rendering dialog
  
 ==== Minimized mode ==== ==== Minimized mode ====
-Upon clicking this last, bottom-most button, the window will convert to minimized view (if it is in full mode, that is):+Upon clicking the third button (which will be replaced with a different version), the window will convert to minimized view (if it is in full mode, that is):
  
-{{:neuroelf_gui:neuroelf_gui_minimized_v09c.png|NeuroElf GUI (minimized)}}+{{:neuroelf_gui:neuroelf_gui_minimized_v09c_110512.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 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:
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   - progress bar area   - progress bar area
  
-==== Cursor position in space ==== +==== Contrast/brightness setting (7) ==== 
-The six spatial coordinate edit fields show and allow to set the current position (cursor/crosshair) in either TAL/MNI spatial convention (coordinate origin is the center of each slice at coordinate [0, 0, 0]) or BrainVoyager convention (coordinate origin is located in the upper, frontal and right "corner", so that the TAL-based center is at BV coordinate [128, 128, 128]). Currently only integer coordinates are supported (but the zoomed view allows for interpolated/non-integer coordinates to be shown of course).+It is now possible to change the contrast and brightness of a voxel-based anatomical object (FMR, HDR, HEAD, VMR) without changing the underlying data. To do so, you can click the **C/B** button, which allows the user to set the minimum value (black) and maximum value (white) for the scaling function, as well as the possible minimum and maximum value (slider range). 
 + 
 +Alternatively, you can click into the slider containing a (vertically aligned) histogram of all non-0 voxels of the dataset. When clicked closer to the maximum slider, the maximum can will be reset to the clicked position (which also works while the mouse button is held down to fine-tune the selection), and when the click occurs closer to the lower slider, the minimum is re-set. 
 + 
 +==== Cursor position in space (8) ==== 
 +The six spatial coordinate edit fields show and allow to set the current position (cursor/crosshair) in either TAL/MNI spatial convention (coordinate origin is the center of each slice at coordinate [0, 0, 0]) or the actual sampling coordinate of the dataset (coordinate origin for BrainVoyager objects is located in the upper, frontal and right "corner", so that the TAL-based center for a full-space VMR dataset is at BV coordinate [129, 129, 129]). Currently only integer coordinates are supported for input (but the zoomed view allows for interpolated/non-integer coordinates to be shown of course).
  
 Additionally, for four-dimensional datasets, a volume selector and edit field allows to change the currently shown volume. Additionally, for four-dimensional datasets, a volume selector and edit field allows to change the currently shown volume.
-==== Configuration of statistical maps ====+ 
 +==== Configuration of statistical maps (9) ====
 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). 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).
  
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 The further controls are The further controls are
-  * the ''alphasim p<.05'' button uses the current map as a template (values non-equal to zero) and runs alphasim with that template as a mask (using the correct spatial resolution) to determine the required cluster size threshold for the more typical uncorrected p-thresholds (results printed in the Matlab console window). +  * the ''alphasim p<.05'' button uses the current map as a template (values non-equal to zero) and runs alphasim with that template as a mask (using the correct spatial resolution) to determine the required cluster size threshold for the more typical uncorrected p-thresholds (results printed in the Matlab console window) 
-  * the ''Clustertable'' button will call the [[vmp.ClusterTable]] method for the currently select map (only for single map selection) and update the configured clusters list as well as the table output field. The checkbox right of the button dis/enables the splitting of larger clusters into sub-clusters, for which the peaks will be reported separately if enabled. +  * the ''Clustertable'' button will call the [[vmp.ClusterTable]] method for the currently select map (only for single map selection) and update the configured clusters list as well as the table output field. The checkbox right of the button dis/enables the splitting of larger clusters into sub-clusters, for which the peaks will be reported separately if enabled; optional setting for the Clustertable output can be set via the **File -> Options -> Clustertable** sub-menu 
-  * the ''MNI2TAL'' checkbox controls whether, for any created cluster table, coordinates are converted from MNI into TAL space/convention (by applying the ''mni2tal.m'' function written by M. Brett).+  * the ''icbm2tal'' checkbox controls whether, for any created cluster table, coordinates are converted from ICBM into TAL space/convention (by applying the [[icbm2tal]] function)
   * the ''TDclient'' checkbox controls whether, for any created cluster table, coordinates are passed on to tdclient, so that for each peak the nearest gray-matter label is looked up   * the ''TDclient'' checkbox controls whether, for any created cluster table, coordinates are passed on to tdclient, so that for each peak the nearest gray-matter label is looked up
   * the ''Interpolate'' checkbox controls whether statistical maps are interpolated into the spatial resolution of the UI (1x1x1 mm) or sampled with nearest-neighbor sampling   * the ''Interpolate'' checkbox controls whether statistical maps are interpolated into the spatial resolution of the UI (1x1x1 mm) or sampled with nearest-neighbor sampling
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   * if the color coding is set to RGB, the colors for positive and negative minimum and maximum values (thresholds) can be configured using the four colored buttons   * if the color coding is set to RGB, the colors for positive and negative minimum and maximum values (thresholds) can be configured using the four colored buttons
  
-==== Output of values ====+==== Output of values (10) ====
 This box simply contains the sampled value at the current (cursor/crosshair) position, both for the selected anatomical and any selected statistical map. This box simply contains the sampled value at the current (cursor/crosshair) position, both for the selected anatomical and any selected statistical map.
  
-==== Time course display ====+==== Time course display (11) ====
 For four-dimension datasets, this area displays the time course at the current (cursor/crosshair) position. A click into the timecourse will also set the volume selector to that position (which works more interactively than using the volume slider, as this requires the mouse button to be released!) For four-dimension datasets, this area displays the time course at the current (cursor/crosshair) position. A click into the timecourse will also set the volume selector to that position (which works more interactively than using the volume slider, as this requires the mouse button to be released!)
  
 {{:neuroelf_gui:main_ui_with_timecourse.png?640|Main UI window with VTC and time course}} {{:neuroelf_gui:main_ui_with_timecourse.png?640|Main UI window with VTC and time course}}
  
-==== Slice display ====+==== Slice display (12a/b/c) ====
 In both the three-slices view and the zoomed one-slice view, any click into one of the slices will set the cursor to the clicked position within the slice. This allows for relatively simply browsing of the dataset. The position will keep updating while the mouse button remains pressed (and the mouse moved). In both the three-slices view and the zoomed one-slice view, any click into one of the slices will set the cursor to the clicked position within the slice. This allows for relatively simply browsing of the dataset. The position will keep updating while the mouse button remains pressed (and the mouse moved).
  
 To reset the slice display to its original position (central coordinate), press the ''r'' key on the keyboard. To reset the slice display to its original position (central coordinate), press the ''r'' key on the keyboard.
  
-==== Surface display ====+==== Surface display (12) ====
 For the surface display, the following viewpoint modifications are supported with the mouse (while the mouse button is pressed within the surface area and remains pressed throughout the mouse motion): For the surface display, the following viewpoint modifications are supported with the mouse (while the mouse button is pressed within the surface area and remains pressed throughout the mouse motion):
   * without any modifier key pressed, the view will rotate (along the Z axes for left/right mouse movement -> longitude/azimuth, and along a perpendicular spatial axis -> latitude/zenith)   * without any modifier key pressed, the view will rotate (along the Z axes for left/right mouse movement -> longitude/azimuth, and along a perpendicular spatial axis -> latitude/zenith)
neuroelf_gui.1304808251.txt.gz · Last modified: 2011/05/07 22:44 by jochen