Export tractography to T1W/T2W images for DBS, focused ultrasound, or surgical navigation

Introduction

DSI Studio can mark tracks or regions on T1W DICOM files for further use in the surgical navigation systems. The following are steps for exporting this information.

Step 1. Generate Tractography


You will need to follow the documentation from Read DICOM, NIFTI, Bruker 2dseq, or Varian FDF Files, Diffusion MRI Reconstruction in DSI Studio (suggest using GQI or DTI), and finally Diffusion MRI Fiber Tracking in DSI Studio to generate the target pathways. 

Step 2. Import T1W/T2W DICOM files

In [STEP T3: Fiber tracking], open the FIB file you get from the previous step and then import your DICOM images using [Slices][Insert T1W/T2W]. You will see how the tractography fused with T1W/T2W images.

You may need to sort and rename DICOM files (see Read DICOM, NIFTI, Bruker 2dseq, or Varian FDF Files) if your DICOM files are from the scanner. This will avoid including other image modalities and make sure that slices are in the right order.


DSI Studio will run a real-time background registration. It may take a while and you can check whether the alignment is good by overlaying local fiber orientation on T1W (see below).  The region window on the left-bottom corner allows you to enable/disable overlap of local fiber orientation. Click it to switch on and off for checking the alignment. You may also need to zoom-in/out to see the details, the shortcut buttons are on the left-upper corner. 


If the alignment is not good, you can manually adjust it using [Slices][Adjust Registration]. Use the "switch view" button to check the alignment.


The mapping result can be saved/loaded using the [Slices][Save Registration] and [Slices][Load Registration] function.

Step 3: Mark targets on T1W/T2W


Make sure that the current slice is the T1W DICOM you loaded, and then use [Slices][Mark Tracts on T1W/T2W] to create bright spots on the T1W slices. 
To save slices back to the original DICOM, use [Slices][Save Slices to DICOM] and select the original DICOM images. DSI Studio will output new DICOM files with "mod" in the prefix of the file name.

You can also manually draw a region (see Diffusion MRI Fiber Tracking in DSI Studio about how to draw regions) and mark the region on T1W/T2W using [Slices][Mark Regions on T1W/T2W]. 
The results can also be saved to DICOM using the same procedure. 


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