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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
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Effect of fiducial marker #611

Open parekhpravesh opened 7 years ago

parekhpravesh commented 7 years ago

Hello,

When using a fiducial marker (such as a vitamin E capsule), there would be hyper-intensities outside the skull. What kind of effect would it have when calculating quality metrics?

Attachment: a run of mriqc on colin27 template with fiducial marker (please note that this was done using an older version of mriqc) effect_of_fiducial_marker

Thanks and Regards Pravesh Parekh

oesteban commented 7 years ago

This is indeed a great question. A wild guess tells me that the fiducial markers will be considered as artifactual intensities since they are usually located within the "hat" mask. Therefore, the dataset will have higher QI1 values than scans without fiducials.

@chrisfilo, do you know if BIDS has any meta key for fiducial markers in the image? It seems to me the easiest way to tell MRIQC where to expect fiducial markers (and dismiss them accordingly).

WDYT?

chrisgorgo commented 7 years ago

I don't think it does. Would you like to propose something at the bids-discussion mailing list?

On Mon, Jul 31, 2017 at 3:38 PM, Oscar Esteban notifications@github.com wrote:

This is indeed a great question. A wild guess tells me that the fiducial markers will be considered as artifactual intensities since they are usually located within the "hat" mask. Therefore, the dataset will have higher QI1 values than scans without fiducials.

@chrisfilo https://github.com/chrisfilo, do you know if BIDS has any meta key for fiducial markers in the image? It seems to me the easiest way to tell MRIQC where to expect fiducial markers (and dismiss them accordingly).

WDYT?

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parekhpravesh commented 7 years ago

@oesteban @chrisfilo thanks...I have just started a discussion on the mailing list.

chrisgorgo commented 7 years ago

Thanks! Much appreciated.

On Aug 3, 2017 8:41 AM, "Pravesh Parekh" notifications@github.com wrote:

@oesteban https://github.com/oesteban @chrisfilo https://github.com/chrisfilo thanks...I have just started a discussion on the mailing list.

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stale[bot] commented 6 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

stale[bot] commented 5 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

parekhpravesh commented 4 years ago

Hello...this is an ancient issue too. I still think that it would be nice if we could have this optional field that would indicate which side the fiducial marker is on but that discussion died out a long time ago.