Possible Bug: Image Orientations

[Tyler Diorio]

Hello,

I'm using the most recent version of the software (6/8 DSI Studio download) and experiencing issues with the orientation of my scans throughout the pipeline. Before using DSI Studio I pre-process an Axial DTI scan with eddy current + topup and register to it's respective Sagittal T1 space. Then I import my DTI (corrected, on Sagittal T1 space) into DSI studio. In Step 2, the GUI opens as a rotated view of my original image so I can apply the following actions to rotate it back to the correct orientation - (1) Image Swap XZ; (2) Image Swap XY; (3) Image Flip X. Then, I open the respective file in Step 3 which shows a different orientation before generating fibers. Lastly, when I export FA as a .nii and view it outside of DSI, it appears rotated once again. I've summed all of this up in the image below:

It seems like the rotations occur during Step 1 and are not fixed when I do the swaps and flips in Step 2. Additionally, I've done the rotate_to T1 image but that also did not fix the rotations, and even made them look moor poorly aligned.

My question is: Is there a way for me to ensure that the final outputs of DSI Studio (fiber directions, FA, etc..) will be the same orientation and space as my original DTI image?

I'm happy to provide the exact commands I'm using as well as a case when I do not perform the Step 2 Image Swaps and Image Flips if that would be helpful.

Thank you,

Tyler

[Frank Yeh]

DSI Studio uses radiology convention so the axial slices will be viewed from the bottom.

Moreover, rotate to T1W is not going to work out because it only addresses minor rotations.

The correct approach is to use image swap or flip to make sure that the Step 2 GUI is showing axial slices from the bottom.

Also, to avoid mirrored results, any slip or swap operation should be applied in pair: see example at https://www.youtube.com/watch?v=XHk_gQN72rU

Hope this helps

Frank

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[Tyler Diorio]

Is there a way to get the Step 2 GUI consistent with the Step 3 GUI and also to be consistent when exporting FA to view in MATLAB with that same orientation? 

Additionally for the Sagittal dataset, it seems that the Step 2 GUI opens as Coronal rather than Axial, is this intended?

Thanks,
Tyler

[Frank Yeh]

Is there a way to get the Step 2 GUI consistent with the Step 3 GUI and also to be consistent when exporting FA to view in MATLAB with that same orientation? 

Step T2 and T3 GUI are consistent, as shown in your figure. Both are rotated sagittal views.

Exporting FA is another story because it depends on how srow in the nifti header is handled.

 

Additionally for the Sagittal dataset, it seems that the Step 2 GUI opens as Coronal rather than Axial, is this intended?

Not at all. 

There is a problem with the source of the data, and it should be fixed using the approach as shown in the youtube video or you have to correct the srow matrix in the NIFTI header before processing using DSI Studio.

Best regards,

Frank

 

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