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Processing pipelines for the HCP
https://www.humanconnectome.org/
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HCP diffusion pipeline #167

Closed rosella1234 closed 4 years ago

rosella1234 commented 4 years ago

Hi

I would like to reproduce 3T and 7T dMRI processing pipeline inserting my own denoising method as a first step. Which pipeline is it suitable for this? Can I just change this initial step? Thanks Rosella

glasserm commented 4 years ago

Why not run your denoising after initial processing (or at least after eddy but before cross-phase averaging)?

rosella1234 commented 4 years ago

What I can read from HCP manual about diffusion pipeline is : Basic preprocessing: Intensity normalization across runs, preparation for later modules. 2. ‘TOPUP’ algorithm for EPI distortion correction. 3. ‘EDDY’ algorithm for eddy current and motion correction.4. Gradient nonlinearity correction, calculation of gradient bvalue/bvector deviation.5. Registration of mean b0 to native volume T1w with FLIRT BBR+bbregister and transformation of diffusion data, gradient deviation, and gradient directions to 1.25mm structural space. Brain mask based on FreeSurfer segmentation. I think I need to start from unprocessed data anyway. best, Rosella

Il giorno mar 3 mar 2020 alle ore 13:05 glasserm notifications@github.com ha scritto:

Why not run your denoising after initial processing (or at least after eddy but before cross-phase averaging)?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Washington-University/HCPpipelines/issues/167?email_source=notifications&email_token=AN42AZNARXSLJUVXOPKLBMDRFTXCJA5CNFSM4LAFUBDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENTHMJA#issuecomment-593917476, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN42AZIKQ7FUTN3A424HN3TRFTXCJANCNFSM4LAFUBDA .

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Rosella Trò Ph.D Student in Bioengineering

System Neuroscience Perceptual System and Imaging Group -SyNaPSI

Department of Informatics Bioengineering Robotics and Systems engineering -DIBRIS

University of Genoa

Via All'Opera Pia 13, 16145, Genova, Italy E-mail: rosella.tro@edu.unige.it

glasserm commented 4 years ago

If you wish to e-mail me privately about what you are doing, I can help you make that determination, but I doubt you would want to denoise data prior to alignment and distortion correction.

rosella1234 commented 4 years ago

Yes I think some preprocessing is mandatory before denoising. If I could be contact you by email that would be great. best, Rosella

Il giorno mar 3 mar 2020 alle ore 14:29 glasserm notifications@github.com ha scritto:

If you wish to e-mail me privately about what you are doing, I can help you make that determination, but I doubt you would want to denoise data prior to alignment and distortion correction.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Washington-University/HCPpipelines/issues/167?email_source=notifications&email_token=AN42AZOACLCPLSNWDI3XFX3RFUAZ5A5CNFSM4LAFUBDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENTPJPI#issuecomment-593949885, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN42AZIVKAY4MRQPMGVN5XDRFUAZ5ANCNFSM4LAFUBDA .

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Rosella Trò Ph.D Student in Bioengineering

System Neuroscience Perceptual System and Imaging Group -SyNaPSI

Department of Informatics Bioengineering Robotics and Systems engineering -DIBRIS

University of Genoa

Via All'Opera Pia 13, 16145, Genova, Italy E-mail: rosella.tro@edu.unige.it

glasserm commented 4 years ago

My e-mail is listed in multiple papers I am the corresponding author of.