gqi fib to nii conversion?

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Dea Garic

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Dec 29, 2022, 7:06:19 PM12/29/22
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Hi Frank, 

Dea again! I hope you've been well. I have always done GQI reconstruction using DSI, but for some newer projects, it would be nice to be able to convert the final gqi fib to nii at the end.. I don't remember this being an option around 2015-2020, but I'm wondering if maybe there's a new update that would make this possible now? 

Best,
Dea

Fang-Cheng Yeh

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Dec 29, 2022, 9:52:34 PM12/29/22
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To nii did you mean output the DWI?
Frank

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Dea Garic

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Dec 30, 2022, 8:53:29 AM12/30/22
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Hi Frank, 

Yes, would it be possible to have an nii file of the gqi fib? Or a GFA/NQA/QA nii for the whole brain? I'm thinking of something similar to the NDI/ODI/csf nii files that MDT and AMICO output for NODDI. 

Let me know if that makes sense. 

Best,
Dea

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________________________________
Dea Garic, PhD
Postdoctoral Fellow
Carolina Institute for Developmental Disabilities
University of North Carolina at Chapel Hill 

Fang-Cheng Yeh

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Jan 1, 2023, 8:39:55 PM1/1/23
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Sorry for the late reply.


Yes, would it be possible to have an nii file of the gqi fib?

It needs an inversion process to convert ODF back to DWI signals.
This is possible but currently not available. (will keep this on my wanted list)
 
Or a GFA/NQA/QA nii for the whole brain?

The export functions are located at GUI [Step T3][Export] or CLI using --action=exp

Best,
Frank
 

Dea Garic

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Jan 12, 2023, 8:11:00 AM1/12/23
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Hi Frank, 

Thank you so much for your very helpful advice! The nii scalars for qa, nqa, and gfa are exactly what I'm looking for. 

The problem I'm having now is that I can output gfa, qa, and rdi, but not nqa. When I try to export nqa, it produces an "ERROR: cannot find nqa in fib.gqi.1.25.fib.gz" 

I also tried running it locally and received the same error. 

The reconstruction command line I'm using is: 
dsi_studio --action=rec --source=*.src.gz --method=4 --param0=1.25 --other_output=qa,nqa,gfa,rdi --output=fib

I've tried it in a few different "outher_output" configurations, and nqa still won't export when I run:
dsi_studio --action=exp --source=*.gqi.1.25.fib.gz --export=nqa

But it works for all other metrics except nqa. I'm running the latest version of DSI studio both on the cluster (dsistudio_latest.sif) and locally (Dec 16th, 2022).  Any advice? 

Thanks again for your help! 

Best,
Dea 

Fang-Cheng Yeh

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Jan 12, 2023, 9:11:04 AM1/12/23
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NQA has replaced QA after the August 2022 version: https://groups.google.com/g/dsi-studio/c/t-kSFxXrGFU?pli=1
Therefore, all current "QA" values are normalized and identical to the previous "NQA."

I am sorry for this change and the hassles caused.
Best,
Frank

Dea Garic

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Jan 12, 2023, 10:02:51 AM1/12/23
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Hi Frank, 

No need to apologize at all! This update makes perfect sense to me, thank you for letting me know. 

Best,
Dea 

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