Importing ROIs misaligned in QSDR analysis

[james.h...@gmail.com]

Hi Frank,

We are having an issue loading ROIs into DSI Studio. We plan to use the following approach

1. During reconstruction, we include a T1w structural image so that it is warped into MNI space with the diffusion data
2. We perform whole brain fiber tracking
3. We import ROIs generated in FreeSurfer (same resolution as the T1w we included in recon), expecting them to be warped into MNI space like the subject data
4. We perform connectivity analysis using the ROIs we have imported

However, our approach fails on step 3. The ROIs we import are misaligned in a significant way (fig1):

It appears the ROIs are translated and collide with a bounding box that truncates them. This is in the Jan-12-2022 version of the software.

When I compare the ROIs and structural image in other software, they appear aligned (fig2):

But note the red text - "Displaying images with different orientations/fields of view!" - could this indicate different sform matrices that are preventing alignment of the ROIs in DSI Studio?

If it would help, I can upload the fiber file and the ROIs.

As always, thanks for the help Frank!

Jim H.

[Frank Yeh]

It seems that the header can be the problem.

Could you upload the fib file, t1w, and the ROI file?

I will see how to fix this.

Frank

[james.h...@gmail.com]

Thanks Frank!

I am uploading a file to DropBox called " ROI_misaligned_sample_data.zip" with the fib, T1w, and ROIs.

Jim

[Frank Yeh]

Hi Jim,

Could you also send me the SRC file? It seems that DSI Studio has
a bug in wrapping the T1W during QSDR.

I will fix it and get back to you.

Best,
Frank

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[james.h...@gmail.com]

Hi Frank - I just uploaded the src ("HCP201_dsistudio.src.gz") to Dropbox.

[james.h...@gmail.com]

Hi Frank,

Sorry to bug you, but I was curious if you were able to make any progress on the bug with the T1W wrapping and ROI import?

I've also tried modifying the ROI file (changing orientation and header info) to see if it would improve the alignment, but no luck so far.

Thanks!

Jim

[Frank Yeh]

I have fixed it several days ago (sorry forgot to inform you)
You may update DSI Studio and re-create the new FIB file to see if it works.
Best,
Frank

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[james.h...@gmail.com]

Thanks Frank! It does appear to be working now.

Jim

[Frank Yeh]

Glad to know it works.

On Thu, Jan 20, 2022 at 11:45 AM james.h...@gmail.com

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