TOPUP preproc

[Mazeaud Charles]

Hello,

I'm trying to run TOPUP/EDDY from the GUI menu in step T2 with an RE phase encoding that I built. Everything seems to work fine and it generates a dwi.corrected.nii.gz file, but it does not generate a new .src file.

The GUI returns to step T2 when it is finished. If I continue with the T2 menu to run the motion correction, it works but does not build a new file.

- Do I have to manually save a .src file after each step and reload it before starting the next step?
 
- Do I have to create a new SRC file at step T1 with the dwi.corrected.nii.gz?

[Fang-Cheng Yeh]

- Do I have to manually save a .src file after each step and reload it before starting the next step?

Yes

 

 
- Do I have to create a new SRC file at step T1 with the dwi.corrected.nii.gz?

No, if you run the correction again in Step T2 from the original SRC file, DSI Studio will check if there exists this nifti file and load it.

Best,

Frank

 

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[Mazeaud Charles]

Thank you very much, it works great!

Best,

Charles

[Mazeaud Charles]

One additional dummy question, 

Does it make sense to aggregate multiples dwi patients in one file to do fiber tracking of a whole cohort in one shot? To perform an anatomical description of fibers passing through several ROIs without two-level comparison?

Is there a automated way through DSI Studio?

 

This

[Fang-Cheng Yeh]

Yes, you may refer to how HCP templates were created (yeh neuroimage 2018 and yeh  Nat Comm 2022).

DSIstudio has all the functions.

Best

Frank

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[Mazeaud Charles]

Hello,

I don't know why I have good fiber reconstruction with DTI and very poor with GQI/QSDR. I tried changing the diffusion sample length from 0.05 to 3.00, but almost all of the cerebellum fibers are still cut off, whatever I do.

Also, the tracking threshold suppresses a large number of fibers. I guess if there was a problem with the preprocessing, the DTI should also be bad, no?

I ask that because is using the QSRD+ODF files the only way to do a population average template (P1)? Or I can build that with my DTI files?

Best regards,

Charles

[Fang-Cheng Yeh]

You can use DSI Studio to get DTI maps but may need other tools to generate an averaged template.

DSIStudio can only construct template using QSDR results.

Best regards

Frank

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