[RESOLVED] Default motion correction option for hcp_fmri_volume (--hcp_bold_movreg)


I have a quick question about the default motion correction option for hcp_frmi_volume:

According to the Notes section from hcp_fmri_volume below, FLIRT is an recommended option for multiband images:

    These last parameters enable fine-tuning of preprocessing and deserve
    additional information. In general the defaults should be appropriate
    for multiband images, single-band can profit from specific adjustments.
    Whereas FLIRT is best used for motion registration of high-resolution
    BOLD images, lower resolution single-band images might be better motion
    aligned using MCFLIRT (--hcp_bold_movreg).

However, HCP pipeline recommends MCFLIRT for processing HCP images (and I presume it would be the same for the images acquired with HCP protocol), which are multiband images:

Do you have any resources that resolve this discrepancy?
That would help me a lot from confusion!

Many thanks,

Hi Minho,

Thank you for spotting this inconsistency. Our logic is that we let HCP Pipelines use their defaults for non mandatory parameters. So indeed, MCFLIRT should be the default for hcp_bold_movreg.

We started using this rule a while ago and it seems like some HCP Pipelines commands that were integrated into QuNex before that time might not fully adhere to it yet. I will change the behavior of hcp_fmri_volume in this case for the next version of QuNex. I will also do another pass over all of the commands to check for any other similar discrepancies. Thanks for pointing this out!

Kind regards, Jure

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Hi Jure,

Thanks for clarification!