[MINC-users] mincreeample transformation problem

[Andrew Janke]

Hi again Colin,

On 4 April 2013 02:40, Colin Shaun Hawco, M <colin.hawco at mail.mcgill.ca> wrote:
> The attached file just showed an axial slice of EPI, with the data shirted forward such that the front of the brain is cut off by the edge of the image.
>
> Because of the size of the mincheaders, i need to split up the message.
>
> T1 image
>
> netcdf p121_anat {
> dimensions:
>         xspace = 160 ;
>         zspace = 256 ;
>         yspace = 256 ;
> variables:
>         double xspace(xspace) ;
>                 xspace:varid = "MINC standard variable" ;
>                 xspace:vartype = "dimension____" ;
>                 xspace:version = "MINC Version    1.0" ;
>                 xspace:comments = "X increases from patient left to right" ;
>                 xspace:spacing = "regular__" ;
>                 xspace:alignment = "centre" ;
>                 xspace:step = 1. ;
>                 xspace:start = -74.777108669281 ;
>                 xspace:spacetype = "native____" ;
>                 xspace:direction_cosines = 1., -0., 0. ;
>         int zspace ;
>                 zspace:varid = "MINC standard variable" ;
>                 zspace:vartype = "dimension____" ;
>                 zspace:version = "MINC Version    1.0" ;
>                 zspace:comments = "Z increases from patient inferior to superior" ;
>                 zspace:spacing = "regular__" ;
>                 zspace:alignment = "centre" ;
>                 zspace:step = -1. ;
>                 zspace:start = 125.30120491982 ;
>                 zspace:spacetype = "native____" ;
>                 zspace:direction_cosines = 0., 0., 1. ;

Well from the above my guess was off, all the files do have regular
spacing (look for regular__ above).

So just to recap, the process for registration is as such:

   mincANTS T1.mnc -> MNI_model.mnc   == T1-model.xfm

   mincANTS EPI.mnc -> T1.mnc  ==  EPI-T1.xfm

   xfmconcat EPI-T1.xfm T1-model.xfm concat.xfm

   mincresample -like EPI_model.mnc -transformation concat.xfm EPI.mnc
EPI_normalised.mnc

?

And if you resample like the MNI_model things are good but if you
resample like the EPI_model things go akimbo?


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