neuroelf_gui
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neuroelf_gui [2010/06/14 22:05] – removing .m from spmmat2prt jochen | neuroelf_gui [2011/05/07 23:02] – added contrast/brightness section, updated image jochen | ||
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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: | ||
- | {{: | + | {{: |
The numbered sections in turn mean: | The numbered sections in turn mean: | ||
- 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/ |
- progress bar area (only visible if a long-running task is executed) | - progress bar area (only visible if a long-running task is executed) | ||
- | - dataset manipulation | + | - drawing |
- view (page) selection buttons and global transformation configuration | - 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) | - 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) | - configuration of statistical map (only VMP format at this time) | ||
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* c) axial/ | * c) axial/ | ||
- | ==== Dataset selection ==== | + | ==== 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 | 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/ | * HDR/NII (Analyze/ | ||
* HEAD (AFNI' | * HEAD (AFNI' | ||
+ | * MSK (BrainVoyager' | ||
* VMR (BrainVoyager' | * VMR (BrainVoyager' | ||
* VTC (BrainVoyager' | * VTC (BrainVoyager' | ||
* as statistical datasets | * as statistical datasets | ||
+ | * CMP (BrainVoyager' | ||
* GLM (BrainVoyager' | * GLM (BrainVoyager' | ||
+ | * HDR/NII (Analyze/ | ||
* HEAD (AFNI' | * HEAD (AFNI' | ||
* VMP (BrainVoyager' | * 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). | 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 |
Once an object is loaded suitable for statistical map overlay, the maps therein can be displayed, also supporting a multi-selection of maps. Additionally, | 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) | * 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, // | * computing a formula on the available map data (VMP format only, // | ||
+ | * 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 |
Below the map area is the listbox that contains the currently configured clusters (comparable to BrainVoyager' | Below the map area is the listbox that contains the currently configured clusters (comparable to BrainVoyager' | ||
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* a table of extracted betas (also showing each subject' | * a table of extracted betas (also showing each subject' | ||
- | ==== 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 |
From top to bottom, these buttons are associated with the following actions/ | From top to bottom, these buttons are associated with the following actions/ | ||
* 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 |
The main UI has three different views: | The main UI has three different views: | ||
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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) | ||
+ | * invoke voxel-based rendering dialog | ||
* 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 | + | 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 | - sagittal view | ||
- coronal view | - coronal view | ||
- axial/ | - axial/ | ||
+ | - drawing tools | ||
+ | - view/page selector | ||
+ | - contrast/ | ||
- current position | - current position | ||
- statistics configuration | - statistics configuration | ||
+ | - progress bar area | ||
- | ==== Cursor position in space ==== | + | ==== Contrast/ |
- | The six spatial coordinate edit fields show and allow to set the current position (cursor/ | + | 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, | ||
+ | |||
+ | ==== Cursor position in space (8) ==== | ||
+ | The six spatial coordinate edit fields show and allow to set the current position (cursor/ | ||
Additionally, | Additionally, | ||
- | ==== 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, | 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/ | + | 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 further controls are | ||
- | * the '' | + | * the '' |
- | * the '' | + | * the '' |
- | * the '' | + | * the '' |
* the '' | * the '' | ||
* the '' | * the '' | ||
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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 |
This box simply contains the sampled value at the current (cursor/ | This box simply contains the sampled value at the current (cursor/ | ||
- | ==== Time course display ==== | + | ==== Time course display |
For four-dimension datasets, this area displays the time course at the current (cursor/ | For four-dimension datasets, this area displays the time course at the current (cursor/ | ||
{{: | {{: | ||
- | ==== Slice display ==== | + | ==== 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). | 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), | To reset the slice display to its original position (central coordinate), | ||
- | ==== Surface display ==== | + | ==== Surface display |
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/ | * without any modifier key pressed, the view will rotate (along the Z axes for left/right mouse movement -> longitude/ | ||
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* '' | * '' | ||
- | ===== File menu ===== | + | ===== Menus ===== |
- | The '' | + | For a list of menu items, please continue |
- | + | ||
- | Additionally, | + | |
- | + | ||
- | Under the '' | + | |
- | * Stats colors (LUT) | + | |
- | * a list of files bundled with NeuroElf to alter the colortable for statistical maps | + | |
- | * Edit LUT palette - this calls up '' | + | |
- | * 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/ | + | |
- | + | ||
- | ===== Analysis menu ===== | + | |
- | Currently this menu has only one working entry: | + | |
- | * Contrast manager - this will bring up the [[NeuroElf | + | |
- | + | ||
- | ===== Visualization | + | |
- | 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]]) | + | |
- | * SPM.mat to SDM conversion ([[spmmat2sdm]]) | + | |
- | * [[alphasim]] | + | |
- | * [[renamedicom|Rename DICOM files]] | + | |
- | * [[spm5_preprojobs|SPM5/ | + | |
- | * [[tdclient]] | + | |
- | * Quality assessment | + | |
- | * [[fmriquality|fMRI quality assessment]] | + | |
- | * [[showspmrparams|Show SPM motion parameters]] | + |
neuroelf_gui.txt · Last modified: 2011/05/18 13:23 by jochen