[Camino-users] questions on reorient: shift in voxel count and identity addition to jacobian

[Alessandro Calamuneri]

Hi Philip,
many thanks for the answers.

Best,
Alessandro

2014-09-10 18:07 GMT+02:00 Philip A Cook <cookpa at mail.med.upenn.edu>:

> Hi,
>
> The offset issue is a legacy thing, internally the coordinate (0.0, 0.0,
> 0.0) is at the edge of the voxel and not the center. Since the shift is
> there, FSL must place (0.0, 0.0, 0.0) at the voxel center, which is how
> most image processing software would do it.
>
> The Jacobian thing is standard, it's done so that an identity transform
> (zero displacement vectors) has a determinant of 1. When you take the log,
> this becomes 0. The log determinant is usually used to express contraction
> (logjac < 0) or expansion (logjac > 0) or no change (logjac = 0).
>
>
>
> On Sep 1, 2014, at 9:34 AM, Alessandro Calamuneri <alecalamuneri at gmail.com>
> wrote:
>
> > I camino experts,
> > I am writing you because I would like to better understand how reorient
> works on tensors. I have checked the source code, and two points are not
> clear to me: first one is that, when using displacement field coming from
> FSL fnirt command, there is a sistematic shifting on voxel position of half
> unit; indeed you typed down
> >
> > double posX = (voxX+0.5)*CL_Initializer.voxelDims[0];
> > double posY = (voxY+0.5)*CL_Initializer.voxelDims[1];
> > double posZ = (voxZ+0.5)*CL_Initializer.voxelDims[2];
> >
> > Why does this shifting occur? Is it an fsl related issue?
> > The other question is coming from jacobian construction. Why do you add
> an identity matrix to the Jacobian after getting directional derivatives of
> displacement field?
> >
> > Best Regards,
> >
> > Alessandro
> > _______________________________________________
> > Camino-users mailing list
> > Camino-users at www.nitrc.org
> > http://www.nitrc.org/mailman/listinfo/camino-users
>
>


-- 
Alessandro Calamuneri
M.Sc., PhD-student in Ricerca Clinica e Traslazionale in Neuroscienze ed
Oncologia
Department of Neurosciences, University of Messina, Italy
Via Consolare Valeria, Policlinico Universitario, 98125, Messina

mail: alecalamuneri at gmail.com
        alessandro.calamuneri at unime.it
        acalamuneri at unime.it
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