Dear Silvia,
Michael is right that the qform from the dicom conversion should represent
your "real" scanner coordinate system, although both the scanner software
and conversion software can fail to give you exactly what you might want (e.g.
scanners can "re-centre" their origin between different scans, which can stop
you easily aligning them).
As for applyxfm, and all the FSL transformation tools, we do use the
"lower left" corner (the 0,0,0 voxel coordinate) as our origin. We also
use specific conventions for signs and orders of rotations, which we
think are reasonable, but are not always the same as conventions used
in other pieces of software (actually the more accurate statement would
be that they are seemingly never the same). So be careful about these
conventions too, as that can make things tricky.
All the best,
Mark
On 7 Feb 2012, at 14:17, Michael Harms wrote:
> Hi Silvia,
> How did you get your data into Nifti format? For example, if you used
> 'dcm2nii', the qform should reflect the transform into the physical
> space of the gradient axes, which it sounds like is what you want.
>
> cheers,
> -MH
>
> On Tue, 2012-02-07 at 12:47 +0000, Silvia De Santis wrote:
>> Hi,
>>
>>
>> We had motion capture cameras installed lately on our 3T and I would
>> like to use the recorded motion to correct my data. I am experiencing
>> two issues:
>> 1) I need the "absolute" scanner origin of coordinates, but if I use
>> FSLHD both the qform and sform are centered at the centre of the FOV
>> rather than in some "real space" and this is an issue because I need
>> all the data to be expressed in a common scanner reference frame
>> 2) When I translate the rotations recorded with the motion capture
>> cameras, I need to express them with respect to the lowest left corner
>> of the FOV to be compatible with APPLYXFM, right?
>>
>>
>> Does anyone have some insights?
>> Many thanks!
>>
>>
>> Silvia
>>
>>
>>
>> *****************************************************
>> Silvia De Santis
>> CUBRIC
>> School of Psychology
>> Cardiff University
>> Tel: 029 2087 0354
>> Fax: 029 2087 0339
>> Web: http://psych.cf.ac.uk/cubric/people/ras.html
>>
>>
>> *****************************************************
>>
>
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