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


DSI Studio allows exporting tractography with T1W as NIFTI file. The NIFTI file can be converted to DICOM (e.g. https://github.com/biolab-unige/nifti2dicomand used as DBS target, focused ultrasound guidance, or surgical navigation. 

The following are steps and tips 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. When doing the fiber tracking, make use of an existing atlas or import your own atlas. There is also an automatic fiber tracking function to help tracking the target.

Step 2. Import T1W/T2W

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

DSI Studio will run a realtime 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

There are two ways to mark targets on T1W/T2W. The first way is using tracks as targets and mark them on the T1W/T2W using [Slices][Mark Tracts on T1W/T2W]. The second way is manually drawing 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]. After marking the target, you can inspect them in the 3D window or region window and save the modified T1W/T2W images as a NIFTI file using [Slices][Save T1W/T2W images...]. To save images to DICOM, you would need to use DICOM format as the original image slices in STEP 2, and save the marked slices using [Slices][Save Slices to DICOM].


  • You can upsample inserted T1W/T2W images using [Slices][Upsample Slices by 2] to achieve a much high target resolution.