Ordering for iotools center-nifti

[Michael Evans]

Hello,

My current pipeline consists of running the t1-volume pipeline and then the pet-volume pipeline.

When I run the t1-volume pipeline it warns me that a subset of nifti files are off center and suggests I run the iotools center-nifti command on the t1w images.

Am I correct in understanding that the t1-volume pipeline will still run anyway? Should I first cancel it, re-center, and then re-run t1-volume? Or does this issue only matter for the pet-volume pipeline afterwards?

If this is the case, I'm wondering if I should just pre-emptively always run iotools center-nifti before the t1-volume pipeline? Is there any harm in doing this to both t1w and PET modalities before running any of the Clinica pipelines?

Thanks so much,

Michael

[Alice Joubert]

Hello Michael,

The warning about center-nifti is triggered when images are not centered. T1-Volume will still run but it becomes an issue with down-processes involving SPM which is the case for PET-Volume. It remains your choice which is why we don't force the user to do it. Normally the center-nifti tool should do nothing to images that are not centered so I don't see any harm in centering them preemptively in this case (could be safe to check).

Hope this helps,

Alice

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