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Subject:

Re: Realignment parameters

From:

"MCLAREN, Donald" <[log in to unmask]>

Reply-To:

MCLAREN, Donald

Date:

Mon, 21 Feb 2011 11:39:14 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (99 lines)

Additionally,

You could exclude TR-to-TR motion that is excessive, by adding a
column of a single 1 in the design matrix for each bad point, but
again there is no standard for a bad point. We've used .75mm
translation and 1 degree rotation. In summary, if you have 5 bad
points, then you will have 5 columns added to your design matrix.

As a side note to the above procedure, the question arises as to how
many bad points are allowable in a single session. We have excluded
runs that have greater than 10-15%  bad points.

Finally, neither motion correction nor motion parameters can correct
for within TR motion, so data inspection is also necessary to make
sure there is no motion artifacts. We usually check the ResMS, spmT,
and beta images. One can also inspect the raw EPI data for artifacts
as well.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General
Hospital and Harvard Medical School
Office: (773) 406-2464
=====================
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On Mon, Feb 21, 2011 at 8:16 AM, Marko Wilke
<[log in to unmask]> wrote:
> Hi Poornima,
>
>> I have searched through the archives for info on acceptable threshold for
>> movement in our analysis, but with no luck.
>
> This is because no-one really knows for sure. There is a rule of thumb that
> "motion exceeding one voxel size" may be bad, but then again, cannot see
> that from the realignment parameters as you will have to combine
> translations and rotations. See the toolbox by Paul Mazaika for an approach
> that does that for you. There also likely is no fixed number as I guess it
> would depend on your data, paradigm, sequence...
>
>> Can any one suggest if we use the realignment parameters as covariates in
>> 1st level, what is the maximum movement (translation, rotation....) that is
>> removed by these steps?
>
> This question I believe cannot be answered, as you do not remove motion, but
> the additional variance associated with it. See Friston et al., 1996, or
> Johnstone et al., 2006, for some hints.
>
>> For example, if a participant has moved say 8mm and 12deg in one block,
>> can we include the participant in the analysis, assuming that using motion
>> regressors in 1st level has taken care of this?
>
> I am used to working with children, but 8 mm and 12 degrees is massive
> motion even in my book. I would not expect the realignment parameters to
> "take care" of this.
>
> Cheers,
> Marko
> --
> ____________________________________________________
> 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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