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Cortical Thickness Tool

• Tv: 3D rep Use this button to initialise a TvTool as a 3D veiwer. This is required for drawing 3D lines (see below).
• Mouse: seq Hold down this button and select the Profile option. Left click on the Sequence Tv at a GM/WM interface (which you should already have determined using the Get GM/WM button). If the position you have chosen coincides with the boundary already determined, the program calculates the direction of the surface normal through the grey matter and the point along this line at which an opposing GM edge is found. If an Imcalc Graph Tv is open, a profile plot of grey matter probability along this line is plotted. If an Imcalc Tv and Imcalc2 Tv are open, 2D interpolated sections of pixel values, extending 2 pixels either side of the line are plotted, where if the line is considered to move in the z direction, then the planes represented are x-by-z and y-by-z.
• Cort params Brings up the parameters dialogue box
• Help At present this does not work.
• Test Boundary Use this to view the results of the GM/WM boundary detection. Install a Mono Tv, push the slice of interest from the Sequence Tool into the Imcalc Tool and pop it into the Mono Tool. Press the Test Boundary button; the results should appear in pink overlaid on the Mono Tv. Adjust the Canny parameters and Grey/White Midpoint (see below) as necessary.
• Cortical Thickness Algorithm:
• Get GM vol In order to run the cortical thickness algorithm, it is necessary to load in both a segmented grey matter volume and the original T1 images. Pressing this button stores the currently loaded sequence (which should be the GM segmented volume) in memory so that the T1 volume can be loaded without losing the segmented volume.
• Remove Skull Install an Imcalc Tv, then press this button. This produces a mask for each slice which excludes the CSF/skull boundary in the GM/WM boundary detection part of the algorithm, as CSF/skull partial volumes have similar intensity values to grey matter. In practice, this is not really necessary because the Talairach atlas regions will tend to exclude the CSF/skull boundary, so any erroneous thicknesses due to this boundary will be ignored. If you do use it, you need to watch the images which appear in the Imcalc Tv. These show (flashing) views of each slice of the brain. It is assumed that there is a continuous band of grey matter encompassing the rest of the brain, and you should see the images fill with red, but the brain should remain black/purple. If any part (particularly around the occipital lobe) does not have a continuous band of GM, and part of the brain fills with red, you will need to increase the Skull Seg parameter value in the parameters dialog box, perhaps in increments of 0.05.
• Get GM/WM Pressing this button results in the GM/WM boundary being determined for all slices of the brain.
• Get Thickness Takes the GM/WM boundary, determines the 3D surface normal at each voxel on the boundary, traverses the GM segmented volume along this direction up to the search extent defined in the parameters dialogue box. If a true edge or a dip is found, the distance traversed to that edge/dip is inserted into a histogram representing the region it is in, according to the Talairach atlas (Please see Tina Memo 2004-007 for more details). In order for this to work, you also need to open the Coreg Tool and specify and input an Air File for the registration parameters to register the image volumes to the Talairach Atlas. In addition, you need to open the Talairach Tool and specify the location of the Talairach atlas, as well as the start of the filenames (the files all start with an X, so you need to specify /pathname/X, eg, /usr/local/Talairach/X ).
• Apply Median Filter This button removes the effect of any spuriously long thickness values, by taking each voxel on the GM/WM boundary, and comparing the thickness value associated with it with the median value of a window of 5 boundary voxels (with the voxel of interest at the central position). If the difference is greater than the Edge Limit parameter (in the parameters dialogue box, default of 4mm), then the value of the voxel under consideration is set to the median. In practice this produces very few false positives and false negatives, but does remove spurious results.
• Plot Regional Thickness Histograms
• Hist: Whole/Left/Right Choose whether you want to view the histogram of the given structure (defined by Hist. No. as described below) for the left hemisphere, right hemisphere or both (whole) hemispheres.
• Hist no: Choose the number of the histogram you wish to view. (See section on Histogram numbers and regions defined for a list).
• Single Hist. If an Imcalc Tv Graph is installed, the histogram of the thickness values in a region is displayed, and summary statistics, comprising the median, number of entries in the histogram, lower quartile and upper quartile, are shown in the tinaTool panel.
• All Hists. Plots the histograms of all the regions, but more importantly writes the summary statistics of all the regions to the tinaTool panel so they can be copied and pasted to other applications.
• Remove Hists. Removes the histograms from memory.
• Graphics Results This allows 2D and 3D visualisation of the cortical thickness results.
• 2D Overlay For the current slice in the sequence tool, displays a 2D overlay of the lines through the GM starting at the boundary defined in this image. Please ensure you set the Sequence Tv as the current Tv, otherwise the overlay will appear on a different TvTool. Note that this is a 2D representation of 3D volume, hence there will be some lines which do not appear to end at valid boundaries. These simply end at out of plane positions. If you wish to interrogate these lines further, please use the Mouse Seq Profile button described above.
• 3D Lines For all voxels on the GM/WM boundary, plots a 3D visualisation of all the lines through the GM. Please ensure the ``threed'' TvTool is the current Tv. This can be installed using the Tv:3D rep button described above.
• GM/WM Boundary Placement Checks It is possible to calculate the difference in grey level between the assumed GM/WM midpoint value and a bootstrapped estimate of the true boundary value if it is assumed that the voxel values either side of the boundary (using the 3D surface normal direction to the boundary) by some distance defined using the extent parameter in the dialogue box are in pure tissue. The average of the intensity values at these positions, minus the GM/WM midpoint values gives the offset values.
• Calculate Offset Calculates the offset as described above, and inserts them into histograms according to region (so, again, requires that an air file registering the dataset to the Talaiarch Atlas has been input in the Coreg tool and that the location of the Talairach lut files has been defined in the Talairach tool).
• Plot Single Offset Plots the histogram of offset values for a region in the Imcalc Graph Tv and writes the offset value of the peak of the histogram to the tinaTool panel.
• Plot All Offsets Plots histograms of offset values for all regions in the Imcalc Graph Tv and writes peak offset values for all regions to the tinaTool panel.

Next: Cortical Thickness Parameters Up: Tool Description Previous: Tool Description   Contents
root 2019-05-21