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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
48 stars 19 forks source link

segmentation error #88

Closed juansanchezpena closed 4 months ago

juansanchezpena commented 1 year ago

Using 0.1.2 container. We saw a segmentation error on the Myelin Mapss and cortical thickness. Screen Shot 2023-02-13 at 2 16 07 PM Screen Shot 2023-02-13 at 2 16 52 PM

I re ran and the artifact persisted. Could you recommend the best way to fix the error (using freesurfer) and how to plug back into pipeline or if you can recommend another solution.

ericfeczko commented 1 year ago

Its probably a segmentation error with the aseg -- haven't seen it in awhile -- revising the aseg and the plugging it back into the pipeline would work, but the pipeline stages don't divide the segmentation from the initial surface generation (e.g. autorecon-cp). Its possible that the hires refinement would eliminate the issue -- but I'm unsure -- you'd need to rerun the PostFreesurfer stage after fixing the aseg.

perronea commented 1 year ago

Side note: There is an unrelated bug in version 0.1.2 that has been fixed in v0.1.3. I just pushed this new version earlier today and I would recommend re-running all your subjects through the last couple stages of this new release with --stage "DCANBOLDProcessing,ExecutiveSummary"

audreymhoughton commented 1 year ago

@juansanchezpena did @ericfeczko 's suggestion above solve your problem? Let us know if you need more information!

LuciMoore commented 4 months ago

@juansanchezpena I'm closing this for now due to inactivity. I agree that this is likely just due to an error in the segmentation (perhaps due to raw data quality issues or needing to use more sophisticated segmentation generation techniques like what we've been developing with BIBSNet. please reopen if you still need assistance!

juansanchezpena commented 4 months ago

No problem thanks

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From: Lucille A. Moore @.> Sent: Thursday, April 18, 2024 9:55:58 PM To: DCAN-Labs/abcd-hcp-pipeline @.> Cc: Sanchez, Juan (NYSPI) @.>; Mention @.> Subject: Re: [DCAN-Labs/abcd-hcp-pipeline] segmentation error (Issue #88)

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@juansanchezpenahttps://github.com/juansanchezpena I'm closing this for now due to inactivity. I agree that this is likely just due to an error in the segmentation (perhaps due to raw data quality issues or needing to use more sophisticated segmentation generation techniques like what we've been developing with BIBSNethttps://github.com/DCAN-Labs/BIBSnet. please reopen if you still need assistance!

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