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

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1

Hi,

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:

Notes:
    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,
Minho

2

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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3

Hi Jure,

Thanks for clarification!

Minho