Hi Thomas,
The rotation matrix is formed as such:
R = Rx.Ry.Rz
and the translations are put in the 4th column.
This matrix multiplies the input coordinates
to form transformed coordinates in the reference
space.
Given the amount of confusion about "radiological"
and "neurological" ordering, I'm not touching
"clockwise" with a barge-pole. You can take any
flirt or mcflirt matrix and get the equivalent
decomposition into parameters using:
avscale --allparams
This way you can find yourself a "clockwise"
one (according to your definitions of this term)
and see what the angles are like!
All the best,
Mark
On 29 Nov 2011, at 04:49, Thomas Yeo wrote:
> Dear Mark (or other FSL experts),
>
> to clarify and expand on this question about in 2009 about the .par
> output of mcflirt, can I confirm that
>
> 1) rot_x is applied first, followed by rot_y, followed by rot_z,
> followed by the displacement (trans_x, trans_y, trans_z)?
>
> 2) And that the rot_x is rotation about x axis in the clockwise
> direction, etc. as suggested by Satra?
>
> Thanks,
> Thomas
>
>
>
>
>
> Hi,
>
> Not quite - they are the parameters you need to align with
> the reference volume (the middle of the timeseries in FSL).
>
> All the best,
> Mark
>
>
> On 9 Feb 2009, at 01:09, Satrajit Ghosh wrote:
>
>> Hi,
>>
>> Thanks. So am I correct in assuming the following:
>>
>> rot_x, rot_y, rot_z, trans_x, trans_y, trans_z
>>
>> rotations in radians and clockwise
>> translations in mm
>>
>> These are scan to scan changes rather than cumulative (like SPM).
>>
>> Cheers,
>>
>> Satra
>>
>>
>> On Sun, Feb 8, 2009 at 1:57 PM, Xinian Zuo <[log in to unmask]>
>> wrote:
>>> the first three columns are rot and last three are trans.
>>>
>>
> Hi,
>
> Is there a specification somewhere for the motion parameter estimates
> (par file) of mcflirt? I'm looking for information such as which
> fields are rotation, translation, what are the dimensions, is it scan
> to scan motion or cumulative, etc.
>
> Thanks,
>
> Satra
>
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