Inplane

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The Inplane view represents data in the format acquired during scanning. It is the default interface called when you type mrVista at the MATLAB prompt.


Contents

[edit] Interface

[edit] Selecting the scan and data type

The data within a session are organized into groups of scans called data types, each of which contains one or more scans. ('Scan group' may be an appropriate name, although the idea for the 'data types' name is that there may be particular methods specific to certain data types. For instance, the newer GLM code produces a 'GLMs' data type, which contain information such as beta weights and residual error that aren't stored in other data types. Generally, though, any analysis can be applied to any data type.) Data overlays are generally stored according to data type and scan, so the view will only show data from the selected group and scan.

Example Inplane Window, showing 4 slices with a coherence map superimposed. The selected ROI (LVO1) is outlined in white.

Therefore, it's imporant to be sure the view is pointed at the data you want to view. You can select the current data type using the popup menu at the upper right of the window. You can select the scan using the slider to the upper left. As with most sliders in mrVista, you can use either the slider to step through scans, or the edit menu in the label underneath to jump to a specific scan.

[edit] Selecting slices

By default mrVista opens on an 'inplane montage' view, which provides two sliders for determining which inplane slices to view. The first slice slider is just below the scan slider to the left of the window; this determines the first slice in the displayed images (the only slice if you're viewing one slice at a time). Below this is a num slices slider, which sets the number of slices to view. (If the first slice plus subsequent slices is more than the total slices in the view, it will just show from the first slice to the end.)

[edit] Zoom Buttons

If you would like to view only a subset of each slice, use the 'Zoom' button located to the lower left side of the window. After selecting, the pointer will change to a crosshairs; you should then select two points which denote the corners of a rectangle in which you want to zoom. The view will refresh, showing only the regions within each slice which lie within that rectangle.

To zoom out and view the whole slice again, select the 'Reset Zoom' button below the 'Zoom' button.


[edit] Viewing data maps

The View Menu contains a number of options for viewing different types of data superimposed over the anatomical images.

[edit] Anatomy and ROIs (no overlay)

This view hides any data overlays, and shows only the underlay image. If the ROI view options are set to show ROIs, they will also be drawn over the underlay.

[edit] Coherence Map

This option shows coherence data from a traveling wave analysis. The data are stored in the INPLANE{#}.co{} field (which is cell of data matrices for each scan) of the global INPLANE{} variable. If this field is empty (a traveling wave analysis ("corAnal") has not been computed using the Analysis menu), selecting this option will have no effect.

The minimum coherence threshold to use when displaying data is determined by the 'cothresh' slider, to the upper right side of the window, below the data types popup.

While originally specific to traveling wave analyses, the .co field and cothresh slider have been co-opted by other analyses, to provide multiple options for thresholding data. For instance, if you compute a contrast map (which by default reflects the -log(p) value of the contrast for each voxel), the absolute value of the map is normalized and mapped to the .co field. This means setting the cothresh slider will restrict voxels whose absolute value is below a certain level, letting you display both highly positive and negative contrasts. For instance, if you run a contrast (left > right visual field) for retinotopic data, and increase the cothresh to around .1, you will see populations of voxels which strongly prefer either left over right stimulation, or right over left, in different colors. This also works well with the 'Bicolor' color map option accessible in the menu Colormap | Parameter Map Mode | Bicolor. Also, the Retinotopy Model code allows you to map arbitrary fields from the model to the .co field.

[edit] Amplitude Map

This option will display amplitude data from a traveling wave analysis. The data are stored in the INPLANE{#}.amp{} field. If a traveling wave analysis ("corAnal") has not been computed using the Analysis menu, selecting this option will have no effect.

The amplitude reflects the amplitude of the best fitting sinusoid in the traveling wave analyses. It is generally used only in viewing traveling-wave data. In Amplitude mode, the 'mapWinMin' and 'mapWinMax' sliders on the right side of the window will restrict voxels according to amplitude. In all other modes, they refer to the more general .map{} (parameter map) field.


[edit] Phase Map

This option will display phase data from a traveling wave analysis. The data are stored in the INPLANE{#}.ph{} field. If this field is empty (a traveling wave analysis ("corAnal") has not been computed using the Analysis menu), selecting this option will have no effect.

For Traveling Wave experiments, the phase field reflects the phase of the best-fitting sinusoid for each voxel. The essence of a traveling wave analysis is that this value tends to vary smoothly from voxel to voxel. So, if you've performed a mapping experiment like a retinotopy experiment, a way to assess if this works is if the colors vary smoothly. (You will probably want to restrict to significant voxels; a cothresh value of around .20 is usually significant and restricts to good voxels, although it's good to test a range of values, and examine things like the level of noise outside the brain, to determine a good threshold for each data set.)

Note that the phase value is expressed in radians and reflects the zero-point crossing of the best-fitting sinusoid, relative to the start of each cycle. This is distinct from radians of visual angle, and to relate this value to the parameter being mapped by an experiment requires consideration of what's being displayed in the experiment over the course of one cycle. There are some tools available to help with this, in the menu Colormap | Set Retinotopy Params..., which will be described shortly.

Like the .co{} field, the .ph{} field is also used for other analyses. The Retinotopy model data can project any field into a ph map. Some of the maps produced by MultiVoxelUI analyses may also project parameters such as voxel reliability into this field, to allow for thresholding by multiple criteria.

[edit] Phase Projected ...

[Rory's not sure what this refers to, exactly. It seems to relate to viewing data from corAnals, but selecting a reference phase which reflects an expected phase for a sinusoid predictor.]


[edit] Mean Map

This option views the mean intensity map (mean over time) of the functionals for each scan. This value is stored in the INPLANE{#}.map{} field. Note that this option specifically looks for the mean map, though other maps may also be stored in the .map field. If a file 'meanMap.mat' is not found in the data directory for the selected data type (e.g., Inplane/Original/meanMap.mat), it will automatically try to compute this map for all scans. You can compute it ahead of time, or only for certain scans, under the Analysis menu.

In viewing traveling wave data, it is sometimes good to load this map as well, and restrict it using the mapWinMin slider, such that the lowest intensities are not considered. This will add an extra criterion for data display / ROI selection which will remove voxels which have a low signal.

[edit] Laminar Distance Map

This option views data reflecting the mean distance along gray matter, and is part of David Ress' laminar analysis tools. [It could use more explanation.]

[edit] Residusal Std. Map

This option views the residual standard deviation from a traveling wave analysis. This value is stored in the INPLANE{#}.map{} field. It may be computed in the Analysis menu under Traveling Wave options. If no map is found (name 'resStdMap.mat' in the current data type folder), will produce a warning and do nothing.

The residual std. deviation provides a measure of the remaining variance after fitting with a sinusoid.


[edit] Parameter map

This option views whatever data are contained in the INPLANE{#}.map{} field for the current scan. If no map is loaded, this option does nothing. All GLM contrast maps, and generalized maps (like the mean map or the spatial gradient map) are stored in the .map field.

[edit] Other View Options

[edit] Changing the Underlay Image

By default, the image on which data maps are projected are the T1-weighted anatomical Inplane images. There is a tool which allows you to change this image. This is accessible via the menu View | Anat Image | Change Underlay..., or from the command line using setUnderlay(view). This tool allows you to switch between the Inplane anatomies, a set of resamples anatomicals using the currently selected Volume Anatomy and Alignment, or the mean time series from one or more scans.

Dialog for changing the underlay image

The available underlays begin with just the T1 anatomies. You can load the others by selecting the "Interpolated Inplanes" button, which will compute the interpolated slices from the volume anatomy based on the current alignment, or the "Load Mean TSeries" button. If you select a new underlay, you can select "use but don't save" to view this underlay for the current inplane window only, or "save as default" to make this underlay the new one for future inplane windows for this session. Note that selecting "save as default" does not erase the other underlays; these are all stored in the .mat file Inplane/anat.mat, under the struct array variable underlay. You can later change the default back to a previous selection.

[edit] Labeling real-world directions on the inplanes

mrVista can label the left/right or anterior/posterior directions of the inplanes, if the anatomies for the inplanes are present as DICOM files in Raw/Anatomy/Inplane, or if the mrSESSION.dirLabel field is set (see below). You can set preferences about the label using the menu View | Anat Image | Set Direction Labels. This allows you to determine whether to label the left-right [default] or anterior-posterior directions, as well as set the size of the label.

If the inplanes were not initialized from DICOM files, but you know the directions from other header information, you can manually set the label by setting the mrSESSION.dirLabel field. Here is an example of what this field looks like.


>> mrSESSION.dirLabel
ans = 
          textRL: 'Right  \leftrightarrow  Left'
          textAP: '(Roughly Coronal/Axial)'
    sagittalFlag: 0

(The '\leftrightarrow' string is TeX interpreter code to render a bidirectional arrow. It's a nice trait of MATLAB that many objects, such as axis labels and titles, can render this code. So, a helpful hint, if you're plotting a variable such as the greek letter sigma, you can label it directly: e.g., ylabel(' \sigma '); .)

[edit] Screenshots

Example Inplane Window, showing 4 slices with a coherence map superimposed. The selected ROI (LVO1) is outlined in white.
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