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Track Visualization


Track with surface rendering


DSI Studio provides several track rendering options for users to customize their preferred visual output. The default setting is tube rendering coded with directional color, but there are also other rendering approaches that may provide better visualization. The cortical surface can be added using [Slices][Add isosurface]. The surface is made transparent by adjusting the opacity level on the [Surface] items in the rendering window. 













Track rendered by diffusion indices

DSI Studio allows for rendering any measurements along the track by changing the option at [Tract][Color] to "Local Indices". 


To use any external supplied measurements, you need first to insert the value map (e.g. a NIFTI file with values) using [Slices][Add slices] and assign a registration matrix using [Slices][Load mapping]. To obtain the mapping, say if the value map is based on T1W images, you can add the T1W by [Slices][Add slices] and save the mapping using [Slices][Save mapping]. The same mapping can be applied to any T1W-based map.

Once the value map is added to DSI Studio, then the drop list in the Color Dialog (as shown in the figure) will have the name of the measurement to renders the tracks according to the supplied value.


Track endpoints rendering

















The track rendering can be the switch to "endpoints" to visualize the termination of fiber tracks.

Insert T1-weighted, T2-weighted or PET images


DSI Studio has a built-in image registration function to present T1w or T2w images along with tractography. To use this function, select [Slices][Insert T1/T2 Images] and assign DICOM or NIFTI files to provide the source data. Image registration will be conducted in the background. Once you load the structural images, DSI Studio starts a background registration. You may need to wait for a while until it reaches a good registration. 

To save the transformation matrix, select [Slices][Save mapping]. The transformation matrix can be exported to a text file. You may also load an external transformation matrix in text format by [Slices][Load mapping]. This will stop the background registration and overwrite it.

To visualize PET image, you need to load an additional PET color map by clicking [Slices][Load Color Map] and select the PET_RGB.txt file (can be downloaded at the bottom of this web page, originally from Dr. Perea Camargo at the Martino Center).
 
Please note that FSL and DSIStudio use different coordinate systems. DSI Studio uses a voxel to voxel transformation matrix, whereas FSL's transformation matrix is mm to mm. To convert the format, one may need to use a scaling matrix to take this into account. Suppose T1 image has voxel spacing: [ 0.4 0.4 0.5 ] and B0 image has voxel spacing: [1.5 1.5 2.5]. We define two scaling matrices A = [0.4 0 0 0; 0 0.4 0 0; 0 0 0.5 0; 0 0 0 1] and B = [1.5 0 0 0; 0 1.5 0 0; 0 0 2.5 0; 0 0 0 1]. Also suppose T1 image size is 520 x 520 x 200. We define a xy-flip matrix C = [-1 0 0 519; 0 -1 0 519; 0 0 1 0; 0 0 0 1]. Finally, let's call the transformation matrix given by FSL, T. Then, the mapping DSI Studio expects is calculated as D = inv(B) * T * A * C.


Rendering the brain surface



DSI Studio is able to render cortical surface and assist localization of the fiber tracts. This requires a high-resolution white matter map in NIFTI or DICOM format. The following is the steps to render the cortical surface.

1. On the top menu, select [Slices][Insert T1/T2]. Then open the white matter mask. The speed button for the same function is located on the top of the 3D window, as shown in the figure to the right. 

2. The loaded images will be linearly registered to the anisotropic map (e.g. FA map) using mutual information maximization. The registration is conducted in the background, and you may need to wait 1~3 minutes until the registration reaches the optimal result.

3. Create an isosurface by selecting [Slices][Add isosurface]. The speed button for the same function is located on the top of the 3D window (labeled +isosurface), as shown in the figure to the right. Select a threshold to create the surface. A higher threshold often results in the smaller surface object, while the lower threshold may loss structural detail. You may need to repeat this step several times until you get a satisfactory result.

4. You may create a cross section of the surface by selecting the drop-down list on the top of the 3D window. The level of the cross section is determined by the slice position. The rendering color and opacity can also be changed using the options under the item named "Surface".
















Rendering a region

Many users find the 3D volume rendering in DSI Studio very useful and are wondering whether it is possible to use it to render  another image dataset. The answer is yes, and this document details the steps that use the 3D engine in DSI Studio to do 3D rendering of any given image dataset. This feature is provided in versions after Jan 2012. Here is the use case example.


      
Input: 3D image volume in Matlab

Say we have an image volume stored in MATLAB as a 3-dimensional matrix, as shown in the figure above. Run the following command to save it as a .fib file.

dimension=size(image);
image=reshape(image,1,[]);
save volume.fib -v4

The above Matlab command stores the image volume in an MAT V4 format that can be loaded in DSI Studio. The maximum loadable size of the image is around 200-by-200-by-200. A volume larger than this may cause an error, and you may use the following code to reduce the size in half for each dimension. (if your image volume is loadable, ignore the following commands).

image = reshape(image,dimension);
image = image(:,:,1:2:dimension(3));
image = image(:,1:2:dimension(2),:);
image = image(1:2:dimension(1),:,:);
dimension = size(image);
image = reshape(image,1,[]);
save volume.fib -v4

Open DSI Studio to load the FIB file. To render the surface, adjust the fiber threshold and select from the top menu [Regions]->[Whole Brain Seeding]. The color of the surface can be changed from the color button in the upper left-hand window, and opacity of the rendered surface can be further adjusted from the options provided in the right options window, as shown in the following figure. You may visualize a cross section of the instruction mentioned in here.







You may also load an ROI and visualize it together with the surface rendering. The ROI can be stored in an MATLAB matrix and use the following command to save it as an ROI file.
 
dimension=size(roi);
roi=reshape(roi,1,[]);
save roi.mat -v4

This ROI file can be loaded in DSI Studio from the top menu [Regions]->[Open], and its color can also be changed from color buttons in the upper left-hand corner window. Changing the opacity of the rendering can help visualize the ROI along with the surface.

Save screen and create rotation videos


You can save the 3D screen using [View][Save 3D Screen]. The rotation videos can be created using [View][Save Rotation Video]

Tips for rendering high-quality images and videos


DSI Studio provides several ways to create figures for publications purpose. To achieve the best quality, please select "High Rendering Quality (Slow)" right under the option window to the right before creating a figure or video. You may also check out the rendering options under [Background Rendering] at the right-hand side, especially the anti-aliasing options (The actual quality may depend on the performance of the graphic card). The following figure shows the difference in rendering quality.





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