neuroelf_gui
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neuroelf_gui [2010/06/10 14:37] – created jochen | neuroelf_gui [2011/05/07 22:44] – adapted panel view to newest version v0.9c jochen | ||
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<code matlab>% bring up NeuroElf GUI | <code matlab>% bring up NeuroElf GUI | ||
- | neuroelf_gui</ | + | neuroelf_gui</ |
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: | ||
- | {{:neuroelf_viewer.png|NeuroElf Viewer (full mode)}} | + | {{:neuroelf_gui: |
+ | |||
+ | After loading or creating some statistical map (and, in this case, the Colin brain VMR), the display has more buttons un-grayed: | ||
+ | |||
+ | {{: | ||
+ | |||
+ | Here is a full-resolution version with numbered areas which are explained below: | ||
+ | |||
+ | {{: | ||
The numbered sections in turn mean: | The numbered sections in turn mean: | ||
- | - sagittal view of the selected anatomical (and/or functional/ | ||
- | - coronal view of the selected anatomical (and/or functional/ | ||
- | - axial/ | ||
- | - 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) | ||
- dataset selection (among loaded objects) | - dataset selection (among loaded objects) | ||
- statistical map selection (multi-select capable) | - statistical map selection (multi-select capable) | ||
- | - configured clusters/ | + | - (a) configured clusters/ |
- | - output of cluster table (only for VMP format at this time) | + | - progress bar area (only visible if a long-running task is executed) |
+ | - drawing tools (only HDR/NII/VMR at this time) | ||
+ | - view (page) selection buttons and global transformation configuration | ||
+ | - contrast/ | ||
+ | - 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) | ||
+ | - output of values at current cursor position (anatomical and statistical values of all selected maps) | ||
- optional time course display if selected dataset is functional and multi-volume (FMR, 4D NII, and VTC) | - optional time course display if selected dataset is functional and multi-volume (FMR, 4D NII, and VTC) | ||
+ | - canonical slicing of anatomical (or functional + optional statistical) dataset(s) | ||
+ | * a) sagittal view | ||
+ | * b) coronal view | ||
+ | * c) axial/ | ||
- | The buttons in the red-marked | + | ==== Dataset selection ==== |
+ | 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 | ||
+ | * FMR (BrainVoyager' | ||
+ | * HDR/NII (Analyze/ | ||
+ | * HEAD (AFNI' | ||
+ | * VMR (BrainVoyager' | ||
+ | * VTC (BrainVoyager' | ||
+ | * as statistical datasets | ||
+ | * GLM (BrainVoyager' | ||
+ | * HEAD (AFNI' | ||
+ | * VMP (BrainVoyager' | ||
+ | |||
+ | Please note: Statistical maps from SPM must currently be imported into BrainVoyager' | ||
+ | |||
+ | 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 ==== | ||
+ | Once an object is loaded suitable for statistical map overlay, the maps therein can be displayed, also supporting a multi-selection of maps. Additionally, | ||
+ | * moving maps within their container (HEAD and VMP format, arrow up and down buttons) | ||
+ | * setting map properties (VMP format only, properties button) | ||
+ | * deleting maps from their container (HEAD and VMP format, trashcan button) | ||
+ | * computing a formula on the available map data (VMP format only, // | ||
+ | * propagating the map condition selection for other subjects (GLM format, ellipse-button) | ||
+ | |||
+ | ==== Configured clusters and table output ==== | ||
+ | Below the map area is the listbox that contains the currently configured clusters (comparable to BrainVoyager' | ||
+ | |||
+ | The buttons next to the cluster list are (from top to bottom) | ||
+ | * mark cluster (sets voxel values in VMR project to specific code) | ||
+ | * restrict cluster (restricts the cluster to either a box or sphere around the first/peak voxel) | ||
+ | * find nearest peak (computes distances between current position and cluster peaks and selects closest peak/ | ||
+ | * zoom on/off (enables a zoomed view on that cluster (potentially useful for screenshots with all three slicing views) | ||
+ | * cluster properties (edit cluster properties) | ||
+ | * delete selected clusters | ||
+ | * load cluster configuration | ||
+ | * save cluster configuration | ||
+ | * extract betas from currently selected GLM for selected clusters (auto-extract is enabled by default) | ||
+ | |||
+ | Below the list of clusters is a multi-line text edit field which contains | ||
+ | * a text version of the clustertable after pressing on the Clustertable button (potentially also showing the nearest gray-matter Talairach label for each coordinate) | ||
+ | * a table of extracted betas (also showing each subject' | ||
+ | |||
+ | ==== Progress bar ==== | ||
+ | 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 ==== | ||
+ | From top to bottom, these buttons are associated with the following actions/ | ||
+ | * browsing mode (drawing disabled) | ||
+ | * 2D drawing mode (drawing within the slice that is clicked into) | ||
+ | * 3D drawing mode (drawing across slices, spherical or cubic around the clicked coordinate) | ||
+ | * floodfill (3D flood-filling of voxels that match the selected criteria) | ||
+ | * marker expansion (expanding the marked | ||
+ | * smoothing (the marked selection is smoothed to remove rough edges) | ||
+ | * undo drawing en/disable (drawing takes back values from the buffer) | ||
+ | * accept changes (copy current version into undo buffer) | ||
+ | * undo (copy undo buffer into current version) | ||
+ | * reload (reload dataset from disk) | ||
+ | * reload marked (reload dataset from disk and mask with marked color) | ||
+ | * reload unmarked (reload dataset from disk and inverse-mask with marked color) | ||
+ | |||
+ | ==== View / Page selection ==== | ||
+ | The main UI has three different views: | ||
+ | |||
+ | {{: | ||
+ | |||
+ | 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/ | * undocking (create a secondary, satellite figure containing the current view, allowing to investigate multiple maps/ | ||
- | * switch to three-slice view (default on startup) | + | * switch to three-slice view (page 1, default on startup) |
- | * switch to sagittal-zoomed view | + | * switch to sagittal-zoomed view (page 2, SAG) |
- | * switch to coronal-zoomed view | + | * switch to coronal-zoomed view (page 2, COR) |
- | * switch to axial-zoomed view | + | * switch to axial-zoomed view (page 2, TRA) |
* 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 | + | * switch to surface rendering view (page 3) |
* minimize/ | * minimize/ | ||
+ | ==== 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 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 | + | {{:neuroelf_gui: |
+ | |||
+ | 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/ | ||
+ | - drawing tools | ||
+ | - view/page selector | ||
+ | - contrast/ | ||
+ | - current position | ||
+ | - statistics configuration | ||
+ | - progress bar area | ||
+ | |||
+ | ==== Cursor position in space ==== | ||
+ | The six spatial coordinate edit fields show and allow to set the current position (cursor/ | ||
+ | |||
+ | Additionally, | ||
+ | ==== 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, | ||
+ | |||
+ | 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/ | ||
+ | |||
+ | The further controls are | ||
+ | * the '' | ||
+ | * the '' | ||
+ | * the '' | ||
+ | * the '' | ||
+ | * the '' | ||
+ | * the '' | ||
+ | * 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 ==== | ||
+ | This box simply contains the sampled value at the current (cursor/ | ||
+ | |||
+ | ==== Time course display ==== | ||
+ | For four-dimension datasets, this area displays the time course at the current (cursor/ | ||
+ | |||
+ | {{: | ||
+ | |||
+ | ==== Slice display ==== | ||
+ | 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). | ||
- | The elements on the left side of the figure | + | To reset the slice display to its original position |
- | ===== File menu ===== | + | ==== Surface display |
- | The '' | + | 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/ | ||
+ | * with the '' | ||
+ | * with the '' | ||
- | Additionally, | + | To reset the surface display |
- | Under the '' | + | ===== Keyboard commands ===== |
- | * Stats colors | + | When no control is currently selected (click between controls, into the background of the figure), the following |
- | * a list of files bundled with NeuroElf to alter the colortable | + | * cursor left/right: for slice-based view change the current |
- | * Edit LUT palette | + | * cursor up/down: for slice-based view change |
- | * Linked browsing | + | * '' |
- | * 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 | + | * '' |
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
- | ===== Visualization menu ===== | + | ===== Menus ===== |
- | Currently this menu has only one entry: | + | For a list of menu items, please continue to the [[neuroelf_gui |
- | * Create montage images - this will bring up the [[NeuroElf | + |
neuroelf_gui.txt · Last modified: 2011/05/18 13:23 by jochen