Bruker dicom data in oblique orientation

[Usha Sinha]

Hi Frank

I am working with Bruker 2dseq data for tracking fibers in rat thigh muscles. The orientation for the slice is parallel to the femur and is close to a coronal orientation (oblique coronal). However, DSI-Studio possibly cannot read the orientation from the 2dseq header since it assigns the acquired coronal-oblique slices to axial orientation. I tried swapping b gradient axes and could get a colormap I expected -- but tracking is off--> the fibers run perpendicular to the image plane (since it assumes it to be axial) rather than in-plane (or close to).

I have tried to use DICOM format from Bruker but DSI-Studio will not load it-- 

Thanks for your help earlier outside the discussion group  and hoping to hear soon from you

Usha

[Frank Yeh]

You may try [B-table][Check b-table] function and see if it works for you.

Frank

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[Usha Sinha]

Hi Frank

Thanks so much.

I had tried that before. It reported correcting by flipping  by .021fx .  It flipped By and Bz and flipped the sign of x. This gave a red hue that made the fibers run in-plane along x-axis. So to get the fibers to run in the y-axis, I switched Bx ad By.   The fibers are now running at an angle to the coronal slice-- 

My question was also that when I had sagittal slices from a Siemens scanner-- human leg muscles, and loaded as DICOM, DSI-Studio resliced into axial and loaded the axials appropriately in the fiber tracking GUI. But for these images from Bruker, DSI-Studio loads the oblique coronals as axials-- I also thought swapping the difusion gradient axes should solve but this slice orientation also may be a source of the problem

Can I upload the 2dseq as well as fiber tracks in a Seed Region in the thigh muscle for various combinations of the diffusion gradient axes

Thanks

Usha

[Usha Sinha]

[Usha Sinha]

Hi Frank

Thanks so much.

I had tried that before. It reported correcting by flipping  by .021fx .  It flipped By and Bz and flipped the sign of x. This gave a red hue that made the fibers run in-plane along x-axis. So to get the fibers to run in the y-axis, I switched Bx ad By.   The fibers are now running at an angle to the coronal slice-- 

My question was also that when I had sagittal slices from a Siemens scanner-- human leg muscles, and loaded as DICOM, DSI-Studio resliced into axial and loaded the axials appropriately in the fiber tracking GUI. But for these images from Bruker, DSI-Studio loads the oblique coronals as axials-- I also thought swapping the difusion gradient axes should solve but this slice orientation also may be a source of the problem

Can I upload the 2dseq as well as fiber tracks in a Seed Region in the thigh muscle for various combinations of the diffusion gradient axes

Thanks

Usha

On Friday, June 27, 2025 at 6:03:09 AM UTC-7 Frank Yeh wrote:

[Frank Yeh]

You may also try flip or swap the image volume, or use DTI as the reconstruction method instead of GQI.
It is likely that the diffusion signals are not good enough, and there is no good fiber resolving power.

Best regards,

Frank

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[Usha Sinha]

HI Frank

I am new to any group postings. My  response or your second response does not show up on the google group, only via my email

1. I am using DTI for recon and not GQI.

2. How do I flip or swap the image volume? within DSI-Studio?

3. I have high SNR -> also while the fibers are not tracking correctly, I do get nice fiber bundles

Thanks

Usha

[Frank Yeh]

2. [Step T2 Reconstruction][Edit][Image Flip/Swap]
3. High SNR does not necessarily have good diffusion contrast, which
is needed to resolve fiber orientations. You can check this using [SRC
Quality Control]. A good contrast should have a value greater than 1.0
Higher the better.

Best,
Frank

[Usha Sinha]

Hi Frank

Sorry for the late reply.

1) I could not find the option of [Image Flip/Swap] in [Step T2 Reconstruction][Edit] (When I select Edit, it comes to Step 2a which is specifying the mask, Step 2b : specify a model (DTI) and 2c Outputs--> there is no [Image Flip/Swap] option::: How do I get to it?

2) I ran the quality control check on the src file: Diffusion contrast is 1.056162 (kind of at the beginning of the good contrast)

Thanks

Usha

[Frank Yeh]

It is located at the top menu's [Edit]