In DSI case, the only difference is that user can only pick a pre-defined gradient table and use
a pre-calculated reconstruction matrix. At this point, we provide two gradient tables, one is 257 (plus 1 b0), the other is 514
(plus 1 b0).
Imaging Model
Select the imaging model as DTI, DSI or HARDI/Q-Ball.
Reconstruction
Select this section to include reconstruction into the workflow. Uncheck it if you only want to do tracking.
Raw data files
Set the directory where raw images are located and pick any one image file from the series. Program will
look for other images from the series within the same directory. All image files must be in one directory.
File type
Display the file type of the raw data. Should be either Dicom or
Analyze.
Gradient table
Select a pre-saved gradient table, or create a new one by clicking the edit button on the right.
Number of directions
Number of diffusion gradient directions. This is determined from the selected gradient table.
Number of b0 images
Number of b0 images at the beginning of the image series.
Image orientation
Image orientation patient. This information is retrieved from dicom header and is used to
determine image voxel order. This may not work in all cases as voxel order varies from
different manufacturers with the same image orientation information.
Output prefix
Set the output directory and filename prefix.
Tracking
Select this section to include tracking into the workflow.
Recon prefix
Set the input directory and filename prefix. This should be the output directory and prefix of the reconstruction step.
Track filename
Set the output filename for the track data.
Mask image
Set the mask image to use. By default the program will use DWI image. But it is not always the best choice.
Mask threshold
Set the low and high thresholds of the mask image to use. NOTE: "Auto" does not always work. If you get a empty track data file, it is
very likely because automatically finding threshold failed. You will need to set it manually and redo the tracking.
Angle threshold
Set the angle threshold for the tracking program.
Apply spline filter
Apply a spline filter to the tracks.
Launch TrackVis automatically
Automatically start TrackVis program and load the track file into it after tracking finishes.
Clear
Clear the output window.
Run
Start processing.
Abort
Abort processing.
TrackVis
Launch TrackVis program.
Close
Close the main window and exit.
Output window
Display the output of the currect process, including error messages.
|