Bspmview By Spunt Manual
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bspmview
bspmview
MATLAB program for
viewing 3D fMRI
statistical images
generated by SPM
Download ZIP
Download TAR
View On GitHub
This project is
maintained by spunt
Contents
1. About
2. Installation
3. Launching bspmview
4. The Main Interface
5. Changing the Interface Appearance
6. Display:Preferences
7. Slice Montage
8. Have Questions?
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About
bspmview is a graphical user interface for overlaying, thresholding, and visualizing 3D statistical
neuroimages in MATLAB. It requires a number of core functions from the MATLAB software Statistical
Parametric Mapping. It has been tested on SPM8+. bspmview was directly inspired by and in some
cases incorporates code from from two other statistical image viewers: xjview and FIVE. The idea
behind bspmview was to integrate and improve some of the great features of these two viewing
programs in an interface that I find to be more intuitive, accessible, and customizable. Most importantly,
all of its features require no additional third-party software (other than SPM, of course). Note that
some features in bspmview will be automatically disabled if you load in a statistical image that was
generated outside of SPM (for instance, in FSL), or if bspmview is unable to locate the model output
files (e.g., SPM.mat, ResMS.nii) associated with the provided statistical image.
Features
reads .img/.hdr, .nii, and .nii.gz
can read non-statistical/non-intensity images (e.g., binary mask, ROIs, or count images)
quickly switch display of contrast sign (+, -, or +/-)
voxelvise and cluster-base uncorrected and corrected image thresholding
automatic anatomical labeling with the Anatomy Toolbox or Harvard Oxford atlases
generate interactive table of labeled activation peaks, and save possibly publication-worthy tables
to CSV
customizable and possibly publication-worthy surface renderings
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Features
customizable and possibly publication-worthy slice montages
save thresholded whole-brain maps or specific clusters as either intensity images or binary masks
save region-of-interest images by growing spheres/boxes around a coordinate (and optionally
intersect the sphere/box with thresholded overlay image)
customizable color maps (different maps, set max/min, reverse)
automatically open Neurosynth in browser to examine connectivity/coactivation maps for current
coordinate
and many other random features...
Installation
1. Download the software
2. Put the bspmview folder either on your MATLAB path or in the "toolboxes" subfolder of your SPM
installation. Note that only the parent folder needs to be on the path. The subfolder "supportfiles" is
added to the MATLAB path whenever you run bspmview.
Launching bspmview
If you put bspmview in the "toolboxes" subfolder of your SPM installation, you will be able to launch
bspmview by selecting it from the "Toolbox:" dropdown menu in the SPM graphical user interface:
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Otherwise, as long as bspmview is on your MATLAB path you can start it from the command line by
entering:
>> bspmview
This will open a file selection dialogue window with which you can select the overlay image you'd like to
display:
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You can also give bspmview filenames for overlay and underlay images as arguments. The following
will display the overlay spmT_0001.img on the default underlay (this example assumes that the image is
in your working directory; otherwise, you'd need to enter the full path):
>> bspmview('spmT_0001.img')
This will overlay spmT_0001.img on to T1.nii:
>> bspmview('spmT_0001.img', 'T1.nii')
The Main Interface
Once bspmview has launched you should see something that approximates this:
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Explore the interface. Click on stuff. Change values and see what happens. Try right clicking on one of
the slice views and you should something like this:
Try selecting Save ROI at Current Location and a menu window should pop up:
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Whoa! Spheres AND Boxes? Customizable sizes? And what's this? I have the option to intersect my
Sphere or Box with the currently displayed (i.e., thresholded) overlay!
Changing the Interface Appearance
If the interface looks wonky (e.g., font sizes are too small) or if you just want to mess with the way it
looks, you can do so from from the leftmost menubar entitled bspmview. For instance, you increase or
decrease the size of the GUI window, or you can scale the font size of all text in the interface either up
or down:
Note the shortcut keys (called "accelerators" in MATLAB), which are displayed for Mac OS X here but
should appear with "Ctrl" in place of the "Command" key (e.g., Ctrl=+ should increase font size).
Display:Preferences
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Given that most of the bspmview functionality should be self-explanatory (and given that I have to get
back to my real job!), I'll end the documentation for now by explaining the fields of the Display
Preferences menu, which you can find under Display in the M enu Bar:
This should bring up a menu that looks like this:
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These preferences allow you to customize a number of display features included in bspmview. Modified
preferences are saved and reloaded the next time you use bspmview. Under Thresholding you can
modify:
Corrected
This controls the corrected alpha to use when doing family-wise error
Alpha
correction
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Under Thresholding you can also modify two parameters that control how many peaks (local maxima)
are identified in the currently thresholded overlay. This will primarily affect the results tables, which
display all local maxima. But it will also affect where the crosshair goes when you select Go to Nearest
Peak from one of the slice view menus. The parameters are:
Peak
This is the minimim distance (in mm) separating the peaks. The larger the
Separation
distance, the fewer the peaks. You may know this by the *Dis variable in the
SPM software.
N
This is the maximum number of peaks to identify per cluster. The smaller the
Peaks/Cluster
number, the fewer the peaks. You may know this by the Num variable in the
SPM software.
Under Anatomical Labeling you can modify:
Atlas
This is the Atlas to grab the labels from (currently the Anatomy Toolbox and Harvard-
Name
Oxford are the only two preloaded into bspmview)
Under Surface Rendering you can modify parameters that control how your surface renderings will
look. Most of the parameters correspond to those present in SurfPlot by Aaron P. Schultz, which is the
function upon which this feature is based:
Surfaces
This controls which of the four views to show (L=Left, R=Right). For instance, the
to Render
default L/R Medial/Lateral will show something like this:
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Surface
This controls the type of surface to render on. The above was created using the
Type
Inflated surface option.
Shading
Set the shading information for the surface
Type
N Vertices
This determines the resolution/quality of the rendering.
Shading M in
Set the min greyscale value for the surface underlay (range of 0 to 1)
Shading M ax
Set the max greyscale value for the surface underlay (range of 0 to 1)
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Add Color
Option to include/exclude colorbar from rendering.
Bar
Round
Rounds all values on the surface to nearest whole number. Useful for binary
Values?
mask images.
Nearest
Only the value from the closest voxel will be used. Useful for mask and label
Neighbor?
images.
Dilate
This will use spm_dilate to slightly dilate the suprathresholded image so that
Inclusive
small or non-surface (e.g., sulcul) activations are visible.
M ask?
Slice Montage
To visualize your thresholded map overlaid on a montage of anatomical slices, use the Slice M onage
function, which you can find under Display in the M enu Bar:
You should now see a pop-up menu that will allow you to select the slice view (sagittal, axial, coronal);
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hide either the color and/or the coordinate labels appearing on each slice; give the color (if not hidden)
a snazzy title; and specify the maximum number of slices to include in each row of the montage:
Pressing OK will advance you to the next challenge you will have to face: Choosing the slices to
display. By default, bspmview automatically provides a representative list of slices containing local
maxima in the thresholded image. Feel free to change, or just go with it knowing that you can easily
delete individual slices from the resulting montage:
If it worked, you should see something approximating the mind-blowing work-of-art presented below:
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If there are too many slices, you can delete individual slices by right-clicking on any individual slice
(when you do this, bspmview will try to automatically re-arrange the montage so it continues to look
super hot). If chose to have labels, you can mess with the size and position of those using the - you
guessed it - *Labels menu.
Have Questions?
Hosted on GitHub Pages
Feel free to shoot me (Bob) an email at: bobspunt@gmail.com
using the Dinky theme
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