Marko,
The optimal choice of a rapid motion threshold is unknown, so after some preliminary experiments we chose 0.5 mm/TR for the default rapid motion threshold in the art_global program. A lower threshold may be appropriate for healthy adults.
Scan to scan motion compares the realignment parameters on successive scans, and is estimated as the RMS of the difference of each translational parameter, plus the difference in each rotational parameter (in radians) multiplied by 65 (assumes voxels near the brain edge are at a 65 mm radius). Thus, RMS is in units of mm. Note other researchers may calculate scan-to-scan motion in different ways. The key point is that after a specific method is defined, then the rapid motion threshold can be adjusted to a suitable level later.
More quantitative research is needed in this area. For now, we suggest looking at the Contrast Movie before and after (or use the SPMd toolbox) to see if the chosen repair method has sufficiently cleaned up the timeseries data.
Best regards,
Paul
----- Original Message -----
From: "Marko Wilke" <[log in to unmask]>
To: "Paul Mazaika" <[log in to unmask]>
Cc: [log in to unmask]
Sent: Friday, October 22, 2010 1:47:50 AM
Subject: Re: [SPM] ArtRepair toolbox
Hi Paul,
I have also used the good (?) old parameter "motion exceeding voxel
size" but I quite like the idea of using the speed of change as a more
meaningful parameter. I have been using my own script to detect motion
from the parameters for a while and would like to include this option.
Based on your experience, what threshold do you accept in terms of "mm/TR" ?
Thanks,
Marko
Paul Mazaika wrote:
> There are few, if any, quantitative rules for the amount of motion
> allowed in an fMRI study.
>
> The 3 mm motion threshold is related to a rule-of-thumb in the
> community that subjects with maximum motions larger than 2 mm or 3 mm
> should be excluded from a study. However, this rule-of-thumb discards
> too many subjects in pediatric and clinical populations.
>
> In practice now, we usually ignore the maximum motion threshold
> because the large maximum motions are usually from rapid motions, and
> instead we test for rapid motion mm/TR above a threshold. The rapid
> motion scans have distortions, realignment errors, and spin history
> effects, and so they are treated as artifacts. Large slow motions are
> treated fairly well by a different function in the ArtRepair package.
> Consequently, we exclude subjects based on too many scans of rapid
> motion rather than an amount of maximum motion.
>
> Best regards, Paul
>
> ----- Original Message ----- From: "Jen
> Pokorny"<[log in to unmask]> To: [log in to unmask] Sent:
> Wednesday, October 20, 2010 4:03:13 PM Subject: [SPM] ArtRepair
> toolbox
>
> I am currently trying to use the ArtRepair5 toolbox and had a
> question regarding setting the motion threshold (mm/TR). I use a
> cutoff of 3 mm for overall movement. Does this 3 mm correspond to the
> motion threshold mm/TR in the toolbox? Is there a standard guideline
> on the parameters one should use for these thresholds? Thank you for
> any help! -Jen
>
>
>
--
=====================================================================
Marko Wilke (Dr.med./M.D.)
[log in to unmask]
Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
=====================================================================
--
Paul K. Mazaika, PhD.
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
Office: (650)724-6646 Cell: (650)799-8319
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