Closed juansanchezpena closed 4 months 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.
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"
@juansanchezpena did @ericfeczko 's suggestion above solve your problem? Let us know if you need more information!
@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!
No problem thanks
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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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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 52 PM](https://user-images.githubusercontent.com/72615316/218552815-b4c5ee19-cf47-457d-8a93-b7de1f7ad402.png)
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.