 Introduction
Open the main project window and select link named "Tractography". Open the ".fib" file to present its fiber information. To the right side, there is a slice window presenting pixels with resolved directions in different color coding and background grayscale FA map. To the left side, there are option panels in the upper corner and the 3D visualization panel. At the bottom, there is a track bar to select slices and also a status bar showing a bunch of information in currently pointed pixel.
The steps to create a tracktography are as follows:
1. Select seeding areas
2. Setup tracking options
3. Start tracking
The information for each process is detailed in the following sections.
Step1. Seeding, Region of Interest, and Region of Avoidance
 First of all, adjust the selection threshold to facilitate seeding or region selection. This threshold is used to filter out regions with low FA values.
To select the seeding area, press the left mouse button to assign the area. To unselect, press right mouse button.
Region of interest(ROI) & Region of avoidnace(ROA)
*Text file, Analyze, and NIFTI format are supported for input seeding, roi, or roa.
End regionThe fiber tracts that end in the "end" region are selected. If two end regions are assigned, then the tracts that connect between then are selected.
Modify regions
You may modify the region by right lick on the region list window and expand the submenu under "modify current region." The modification includes shitting the region in x, y, or z direction. Flip x, flip y, or flip z correct the orientation problem. There are also expansion function that expand the current region. Other functions include erosion, smoothing , negate, and defragment.
Load region from anatomical structure
DSI Studio provides a handy list of well-known anatomical structures that can be added to the region list (click the combo-box showing "amygdata"). The atlas are from the Talairach Label Data, and the spatial mapping are obtained by first linearly register the anisotropy map to the NTU-90 anisotropy map in the ICBM-152 space (MNI space) using mutual information minimization, followed by non-linear transforming the MNI coordinate to Talairach atlas.
Step2. Setup Tracking Parameters
This parameter determines
the threshold for fiber termination and eliminate false fibers. In DTI images, FA is used as the index for the filter to
determine the fiber threshold. In DSI, QBI, GQI, the QA values are used. The definition of QA is documented in the GQI paper [3].
Max angleThis threshold
serves as a termination criterion. If two consecutive moving directions
have crossing angle above this threshold, the tracking will be
terminated.
Step sizeStep size defines the moving distance in each tracking interval. This unit is in minimeter scale.
Smoothing
Smoothing serves like a "momentum". For example, if smoothing is 0, next moving direction is independent of the previous propagation direction. If the smoothing is 0.5, each moving direction remains 0.5 "momentum", the previous propagation vector. This function makes the tracks appeared smoother. In implementation detail, there is a weighting sum on every two consecutive moving directions. For smoothing value 0.2, each subsequent direction has 0.2 weighting contributed from the previous moving direction and 0.8 contributed from the income direction. To disable smoothing, set its value to 0. Length ConstraintLength Constraint filters out the tracks that are either too short or too long. Random Initial Direction v.s. Main initial direction If the starting point has more than one fiber population, the tracking method has to determine which fiber population will be selected to perform tracking. Two options are available. The first one is to take the direction of the most prominent fiber population as the initial direction. Another choice is to start from a randomly selected fiber direction in the starting voxel.
InterpolationThe interpolation method used in estimating the fiber orientation. Streamline
tracking method [1][2] is the default method for fiber tracking.
Runge-Kutta method[1] is a higher order tracking method similar to the
default Euler approach. 5000 Tracts v.s. 5000 SeedsThis tracking plan determines when the tracking should stop. The default options is to keep seeding until the total amount of fibers reaches the number. (some fibers will be eliminated due to length constraint, ROI, ROA, End point....). Another option is to have a fixed number of seedings, but the generated fibers may be less.Thread CountDSI Studio supports multithread fiber tracking, which can boost the performace on computer with multiple core CPU. Assign the thread count in accord with the possible computation power to obtain the highest efficiency.
Step3. Perform fiber tracking
Click the start tracking button to perform tracking, and input the tract count or the seeding number. The tracking result can be saved as text files, which stores the coordinates of each fiber track. The coordinates of a fiber track are stored in a line, which has format of "x1 y1 z1 x2 y2 z2 ... xn yn zn". The result can also be exported as TrackVis .trk format or matlab format.
*In DTI dataset, the false fibers are filtered out by
their FA values.
*In DSI, QBI, and GQI with local maximum, the false
fibers are filtered out by its distribution value in the ODF.Reference[1] Basser, P.J., Pajevic, S., Pierpaoli, C., Duda, J., Aldroubi, A., 2000. In vivo fiber tractography using DT-MRI data. Magn Reson Med 44, 625-632.
[2] Wedeen, V.J., Wang, R.P., Schmahmann, J.D., Benner, T., Tseng, W.Y., Dai, G., Pandya, D.N., Hagmann, P., D'Arceuil, H., de Crespigny, A.J., 2008. Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers. Neuroimage 41, 1267-1277.
[3] Yeh FC, Wedeen VJ, Tseng WY. Generalized q-sampling imaging. IEEE Trans Med Imaging 2010;29:1626-1635. |
