Amy,
you should keep that detecting and dealing with motion are two separate
things. Your first question was on detecting, and defining, "bad"
motion. To this effect, I think Helmut graciously provided several hints
with regard to using total displacement instead of translation only,
using scan-to-scan instead of motion-with-reference-to-first motion etc.
The question that you are now posting refers to how to use artrepair,
for which I think their manual and publications is a better starting
point. But to give you a few more concrete replies:
> If yes, What should be the min. number of affected volumes for an fmri
> analysis?
Ideally, there would of course be no volumes to correct.
> Is there any formula to detect it?
The number of "volumes to repair" will depend on the thresholds you set
before you start.
> Otherwise, in my case, if the number of affected volumes is less than 5,
> shall i use the data for further analysis?
That will depend on your threshold and on your data.
> I have seen a repair option which will despike the data and give us new
> volumes with prefix 'v'. Can I preprocess the data again and include
> for further analysis?
I will defer to the artrepair documentation for that.
Cheers,
Marko
> On Tue, Jun 24, 2014 at 9:03 PM, Helmut Nebl
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> When it comes to head motion most of the standard fMRI papers refer
> to overall motion/displacement, measured from the first to the last
> volume. The criterion is typically ~3 - 5 mm or in other words,
> motion within the size of a voxel. Unfortunately this doesn't tell
> us much about data quality, as subjects might constantly be shaking
> their heads/shivering, which often results in rather drastic
> artefacts. This is probably more problematic than the overall motion
> (which is going to affect the data quality to some extent as well of
> course, reduced SNR, losing voxels from analysis if subjects moved
> out of plane, geometric deformations due to inhomogenous magnetic
> field).
>
> Artrepair plots estimated motion between successive volumes ("fast
> motion", scan-to-scan motion). The default criterion is 0.5 mm/TR.
> Similar thresholds or even more conservative ones like 0.3 mm/TR
> have frequently been employed in the context of resting state fMRI
> for the last couple of years. So in your case, as the run is short
> and the number of affected volumes large, the run might have to be
> rejected. There are different opionions on how to treat data sets
> like that, some of them try to replace the "bad" volumes with a mean
> or some interpolated data, others add regressors to the design
> matrix, others discard these subjects entirely. In any case you
> should check whether motion is related to some other variable, as
> you might introduce some bias (for example larger head motion in
> patients).
>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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