Hi Saad,
you're right (of course). Although I mentioned the 6 additional dofs, I
forgot about them contributing to the resulting transformation matrix.
With all due respect,
Niklas
Saad Jbabdi wrote:
> Hi Ed and Niklas,
>
> This is not actually quite true:
>
> 1. if you want to extract the rotation component of the FLIRT matrix,
> you need to use avscale.
>
> 2. FSL4.1.5 has a script that does all that for you. It is called
> rotate_bvecs, and it is based on a donation from Martin Kavec.
> Unfortunately, it has a little bug. If you want to use it you will have
> to edit the text and replace "done" with "fi" at the beginning of the
> script (when it is testing whether it is going to over-write the ouput
> file). Sorry!
>
> Cheers,
> Saad.
>
>
> On 28 Jan 2010, at 13:10, Niklas Stein wrote:
>
>> Hi Ed,
>>
>> there has been some discussion regarding this issue. Since eddy_correct
>> uses motion correction with 12 dof, rotation (as well as shears,
>> skews) is included. You can easily rotate the bvecs by applying the
>> top left 3x3 submatrix of each 4x4 matrix in the .ecclog file to the
>> corresponding bvec. This can be performed either in Matlab or - with
>> sufficient experience - e.g. a shell- or perl script.
>> AFAIK, in FSL this is, however, not yet implemented.
>>
>> With all due respect,
>> Niklas
>>
>> Ed Gronenschild wrote:
>>> Hi,
>>> I'm wondering if in eddy_correct the motion correction also
>>> involves rotation. If that is the case than also the b vectors
>>> should be rotated.
>>> Ed
>>
>>
>> --
>> ----------------------------------------------------------------------
>> Dipl.-Phys. Niklas Stein
>> ----------------------------------------------------------------------
>> Institut für Systemische Neurowissenschaften
>> Universitätsklinikum Hamburg-Eppendorf
>> Martinistr. 52, Haus W34
>> D-20246 Hamburg, Germany
>> Tel.: +49-40-7410-57882
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> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
>
--
----------------------------------------------------------------------
Dipl.-Phys. Niklas Stein
----------------------------------------------------------------------
Institut für Systemische Neurowissenschaften
Universitätsklinikum Hamburg-Eppendorf
Martinistr. 52, Haus W34
D-20246 Hamburg, Germany
Tel.: +49-40-7410-57882
Fax.: +49-40-7410-59955
mail: [log in to unmask]
http:/www.uke.uni-hamburg.de/institute/systemische-neurowissenschaften
----------------------------------------------------------------------
Time ferðast mun hafa gert flóknari málfræði.
----------------------------------------------------------------------
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/\ * against html mail and vcards *
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Please avoid sending me Microsoft Office files as attachments.
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--
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg
Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Prof. Dr. Dr. Uwe Koch-Gromus
|