[Gate-users] Voxelised source problem with ASCII input

[Simon Stute]

Hi David,

>From my knowledge, the bug for ascii description of voxelized sources has
not been yet fixed.
>From my point of view, managing interfile images is much more convenient (or
any binary one), at least for visualization purpose, as many viewers cannot
open ascii images.
When you use interfile input, you do not have to describe it as a slice
sequence like you said. You just have to make a 3D image in unsigned short
int format, that contains labels. Then with your translator, you tranform
labels in activity amount in each voxel.
I give you there, the most simplified interfile header that contains enough
informations to be used with GATE.


!INTERFILE :=
!GENERAL DATA :=
!data offset in bytes := 0
!name of data file := your_image_in_unsigned_short_int_format.i33
;
!GENERAL IMAGE DATA :=
!total number of images := your_number_of_slices
imagedata byte order := LITTLEENDIAN
;
!number of images/energy window := your_number_of_slices
!matrix size [1] := your_number_of_pixels_along_x_axis
!matrix size [2] := your_number_of_pixels_along_y_axis
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := the_pixel_size_along_x_axis_in_mm
scaling factor (mm/pixel) [2] := the_pixel_size_along_y_axis_in_mm
!number of slices := your_number_of_slices
slice thickness (pixels) := the_slice_thickness_in_mm
!END OF INTERFILE :=


It should do the job.
When the bug for ascii description will be fixed, I will let you now.

Good luck,
Simon

On Wed, Apr 13, 2011 at 5:29 PM, David Oxley <d.c.oxley at rug.nl> wrote:

> Dear all,
>
> I am trying to implement a voxelised source of positrons into a cylindrical
> PET scanner using the ASCII method of defining the source and a linear
> translator.
> my question follows on from a discussion in the archives between Simon
> Stute and Ismet Isnaini (
> http://article.gmane.org/gmane.comp.science.opengate.user/1356/match=voxelized+source+ascii,
> last post 22-Feb-2011) where they concluded reading in a voxelised source
> using the ascii method had a bug in it.
>
> I am not sure if I am seeing the same bug, but I am not sure how GATE knows
> my voxel size and I see large amounts of my data are compressed into the
> early entries of my source.
>
> First, I am wondering if there have been any developments on this bug as
> using an ASCII file really sounds much easier.
>
> If not, then I was hoping for more information about this InterFile
> alternative. In the voxelised source section of the manual it appears there
> is only one interfile, in this case hof.h33. But earlier in the manual there
> is a link to
> http://www.colin-studholme.net/software/rview/rvmanual/fileform.html#interfile, where there is talk of a header and a different image for each slice. I
> want my source to be a matrix, 100 x 100 x 100 voxels with a voxel size of
> 1mm x 1 mm x 1mm and I know what the activity should be for each of the
> voxels.
> Does this mean if I have an ascii file  with 100^3 entries, I need to make
> 100 images ending in .IMG for the InterFie format? Are these saved as binary
> or ascii? Is the header binary?
>
> Perhaps someone has come across this problem before or knows more about
> this InterFile format than I do.
>
> Just finally, I would rather not use the InterFile format, if someone has
> fixed the bug or has been able to use the ascii voxelised source without
> problems, I would greatly appreciate their help.
>
> Thanks in advance to you all for taking the time to assist.
>
> Kind regards,
>
> Dave
>
> =================================
>
> Dr. David Oxley
>
> Postdoctoral Researcher
> Kernfysisch Versneller Instituut
> Zernikelaan 25
> NL-9747 AA Groningen
> The Netherlands
>
> d.c.oxley at kvi.nl
> d.c.oxley at rug.nl
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