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Loading Time Course Volumes Loading binary volume Overlays and Time Course data is similar. Use the '''File->Load Time Course...''' command to load a time course volume. TkSurfer requires functional volumes to be in binary volume format. It will look for a header file with the same stem as the slice data or just guess the dimensions from the bfile. You need to specify the directory of the data, the stem, and optionally, a registration file. The format of a bfile name looks like this: |
The source data is a volume. The surface is intersected with the volume in real space, so the volume needs to be registered to the surface somehow. Only some volume types (namely the binary volume type, .bshort or .float) have header data which describe how additional frames should be interpreted as time points or conditions. Some can have multiple frames but don't break them into conditions, so they are just interpreted as time points in the same condition. TkSurfer will do its best to guess the proper format for you. |
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/path/to/data/stem_000.bfloat [[BR]] /path/to/data/stem_000.bshort |
== Loading Time Course Volumes == |
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| The numbers go from 0 to the number of slices minus one. The 'stem' represents any text that appears before the underscore before the number in the bfile. | Loading volume Overlays and Time Course data is similar. Use the '''File->Load Time Course...''' command to load a time course volume. TkSurfer requires functional volumes to be in a volume format; the .w format is not support. You must specify a registration type. These are the options: |
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| You can specify a registration file to use. If you do not, TkSurferwill look in the same directory as the bfile data for a file called register.dat. A registration file is a matrix that defines the translation between anatomical RAS space and functional RAS space. TkSurfer uses this to align the functional volume with the anatomical volume. | '''Specify registration file:''' If you have a register.dat file, probably generated by TkRegister, use this option to specify it. The file contains a transformation matrix, some information about voxel size, and a rounding method. |
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'''Find registration in data directory:''' If you have a register.dat file in the same directory as the data file, use this option to automatically look in that directory. '''Calculate identity matrix:''' If the functional volume is in the same alignment as the anatomical, or you do not with to register the functional volume, use this option. It will calculate a proper "identity" matrix based on the paramters of the functional and anatomical volumes. |
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Time Course
The Time Course is a binary volume with multiple time points or conditions. The data is displayed in a graph so that all time points can be seen for a given vertex. When a vertex is clicked, the corresponding voxel is found in the binary volume. TkSurfer graphs the data for all time points at the chosen vertex.
The source data is a volume. The surface is intersected with the volume in real space, so the volume needs to be registered to the surface somehow. Only some volume types (namely the binary volume type, .bshort or .float) have header data which describe how additional frames should be interpreted as time points or conditions. Some can have multiple frames but don't break them into conditions, so they are just interpreted as time points in the same condition. TkSurfer will do its best to guess the proper format for you.
Loading Time Course Volumes
Loading volume Overlays and Time Course data is similar. Use the File->Load Time Course... command to load a time course volume. TkSurfer requires functional volumes to be in a volume format; the .w format is not support. You must specify a registration type. These are the options:
Specify registration file:' If you have a register.dat file, probably generated by TkRegister, use this option to specify it. The file contains a transformation matrix, some information about voxel size, and a rounding method.
Find registration in data directory: If you have a register.dat file in the same directory as the data file, use this option to automatically look in that directory.
Calculate identity matrix: If the functional volume is in the same alignment as the anatomical, or you do not with to register the functional volume, use this option. It will calculate a proper "identity" matrix based on the paramters of the functional and anatomical volumes.
The Time Course is displayed in a separate graph window. The graph will only be shown if the Time Course volume has more than one time point. Clicking on a vertex in the Display Window finds the corresponding functional voxel based on the registration and displays the values at that voxel for all time points in the graph window.
If there are multiple conditions defined in the header file, each condition will show up as a separate line in the graph. The legend on the right side of the graph window displays what line corresponds to what condition. By moving the mouse over a condition label in the legend, the corresponding line in the graph will be highlighted. This is useful for picking out one condition in a crowded graph.
You can also zoom into the graph. Click and drag with button 2 to draw a box around the area of interest. The graph will be resized around that box. Click with button 3 to zoom back out.
You can specify an average area to graph in two ways. You can click the vertices you want, marking them, and then choose Tools->Graph Marked Vertices Avg to graph the average. (Note that loading a patch marks vertices, so you can also graph the average of a path this way.) You can also load a label and graph the average of it with the Tools->Graph Label Avg.
The contents of the graph window can be written to a Postscript file with the Tools->Save Graph to Postscript File... command. It can then be included in another document or printed.