Hi,
We use the average rms displacement over a spherical ROI, as
calculated with rmsdiff and described in
http://www.fmrib.ox.ac.uk/analysis/techrep/tr99mj1/tr99mj1/index.html
All the best,
Mark
On 5 Nov 2010, at 02:57, Xiaozhen You wrote:
> Hi Mark,
> Is there a formula for the mcflirt estimated mean displacement (the
> summary figure of prestat) related to Rx, Ry,Rz, Tx, Ty, Tz?
> I couldn't find the document that talks about it.
> Thanks!
> Xiaozhen
> On Thu, Sep 30, 2010 at 12:16 AM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Dear Leo,
>
> There is a mapping between the par and the mat files but it
> is not simple and unless you *really* need to know then I
> would advise not bothering with it.
>
> To regress out motion the simple thing to do is to use the
> parameters (from the .par file) directly as regressors.
> This is most easily done in FEAT using the GUI (there is
> a single button) but you can import the .par file as columns
> in a design matrix in any other GLM too.
>
> As to your last question, the parameters are:
> Rx Ry Rz Tx Ty Tz
> where R is a rotation (angle in radians) and T is
> a translation (in mm).
>
> All the best,
> Mark
>
>
>
> On 29 Sep 2010, at 17:59, Yiou Li wrote:
>
> Hi,
>
> I checked the history threads and Couldn't find the following question
> about McFlirt being addressed.
>
> Could any expert on McFlirt/Flirt kindly advise?
>
> Best,
> Leo
>
>
> ---------- Forwarded message ----------
> From: Yiou Li <[log in to unmask]>
> Date: Tue, Sep 28, 2010 at 3:42 PM
> Subject: Question about MCFLIRT output transformation
> To: FSL - FMRIB's Software Library <[log in to unmask]>
>
>
> Hi all,
>
> I performed a 6 DOF of mcflirt on a function MRI dataset and asked for
> output transformation as well as the parameters (i.e., -mats and
> -plots are both used).
>
> I checked the first line of the .par file:
>
> -0.0198375 -0.00176798 -0.0073474 -0.0507674 -0.458798 -0.553456
>
> and the first mat file (MAT_0000)
>
> 0.999971 -0.007347 0.001768 0.533133
> 0.007381 0.999776 -0.019836 0.187519
> -0.001622 0.019849 0.999802 -2.275521
> 0.000000 0.000000 0.000000 1.000000
>
> The questions are:
> 1. Is there is correpsondence between the lines of .par and the MAT
> data? If so, how is the mapping?
>
> 2. To regress out the motion effects, should the lines of .par be used
> and what are the specific meanings of each column? (e.g., rotation,
> translation etc.)
>
> Your input is appreciate!
> Leo
>
>
>
>
> --
> Xiaozhen You, PhD
> Developmental Cognitive Neuroscience Lab
> Georgetown University
> 401 White-Gravenor
> 3700 O Street, NW
> Washington DC 20057
> [log in to unmask]
> 202-687-9133/
> 202-687-8223
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