DTI in skeletal muscle - registration and fibre tracking termination condition

[Shihan]

Hi Frank,

Thanks for the software.

I'm currently using DSI Studio for fibre tractography in skeletal muscles. 

T1W images were inserted during Step 3 as an anatomical reference. After the automatic registration, there were some biases between the T1W image and the DTI data, as shown in the attached picture. I wondered whether it's due to the inaccurate mask developed in Step 2. (I used DTI analysis to calculate FA). I tried to adjust the registration matrix but this only got little effect.

Is it possible to draw the mask manually in Step 2. Or could you recommend some tools to draw the mask which can be imported into DSI Studio?

I drew the ROI in axial planes of T1W images and exported the ROI as txt files. It seems that the voxel coordinates were in the dimension of DTI images. Could the coordinates be saved and imported as txt files in T1W coordinate dimension? (Just for convenience since registrationmatrix can be used to do the coordinate transformation)

Last question is that is it possible to import a 3D mask (such as the muscle surfaces) into DSI Studio, and use this mask as a termination condition during fiber tracking?

Thanks for your time,

Shihan

[Frank Yeh]

The problem is due to limited resolution of DWI.

One solution is use [Step T2][Edit][Rotate to T1W...] to upsample it to the T1W space.

You may give it a try and see if it works.

Frank

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[Shihan]

Hi Frank,

Thanks for your reply. It works!

Another question on fibre tracking: Is it possible to import a 3D mask (such as the muscle surfaces) into DSI Studio, and use this mask as a termination condition during fiber tracking? Or could we generate surface masks from the fibres in DSI Studio and export these masks?

Thanks for your time,

Shihan

[Frank Yeh]

  Sorry for my late reply.

As per your questions:   

 

Another question on fibre tracking: Is it possible to import a 3D mask (such as the muscle surfaces) into DSI Studio, and use this mask as a termination condition during fiber tracking?

Yes, you can do that.

 

Or could we generate surface masks from the fibres in DSI Studio and export these masks?

It would be "end point", which is under [Tract][Tract to end point], but this may not work well in your data.

Best,

Frank

 

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[Shihan]

Hi Frank,

Thanks for your reply.

I tried [Tracts][Tracts TO ROI] and it works. A mask was generated that wrapped all the muscle fibers.

For the first question on using a self-defined mask as the termination condition, I wondered which module should I use. I tried [Tracts][Filter Tracks by ROI/ROA/End], and the resultant fibers seem to be the same. Or should I import the surface mask and change its type to 'End' or 'Terminative' in Step T3a: Assign Regions?

Thanks for your time!

Best regards,

Shihan