[Rtk-users] use RTK to perform CBCT reconstruction of short scan

[Simon Rit]

On Thu, Jan 16, 2014 at 4:21 AM, Patrick Langechuan LIU
<liulangechuan at gmail.com> wrote:
> Thanks, Jan and Simon!
>
> I really appreciate your fast reply and kind help. With your guidance I
> finally get the reconstruction tool rtkfdk to work after experimenting it
> for several hours. Now I have some new questions regarding this tool.
>
> 1. one of the options for rtkfdk is the --spacing, with default value set to
> 1. Correct me if I am wrong, I suppose this specifies the spatial distance
> between elements of the reconstructed 3d matrix (in unit of mm), but does
> this also corresponds to the thickness of projection images used to
> reconstruct that slice? In other words, if there are two reconstructions,
> with options:
> case 1: (--spacing 0.25,1.25,0.25  --dimension 1024,1,1024)
> case 2: (--spacing 0.25,0.25,0.25  --dimension 1024,5,1024)
>
> Is it true that the single slice in case 1 is equivalent of the summation of
> the 5 slices of case 2, or equivalent to the central slice (3rd one) in case
> 2?
No, it's not true. It defines the position of the voxels which does
not mean that it will sum the 5 slices. In your example, the central
slice of case 2 equal the single slice of case 1, not the sum.

>
>
> 2. another option is the origin. I am not sure I totally understand why this
> option is specified as
> --origin -127.875,30,-127.875
> in the 3rd step of the following varian recon example in wiki.
> http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction
>
> My guess is that 30 is needed because only one slice 30 mm off center is to
> be reconstructed, and -127.875 is to ensure x-y direction is "centered"
> (which equals to the default value)? It is a bit odd to me that the default
> origin value is not 0,0,0.
>
> Could anybody comment on these two points? Or direct me to the place where I
> could learn about these details?
You should study a bit ITK for this, it's not a RTK-specific question.
In a few words, the spatial positions of voxels in ITK is defined by
the origin, the spacing and the direction. The origin is the
coordinate of the first voxel in memory, i.e., the inferior corner of
your image in every direction (inferior assumes positive spacing and
identity directions). So if you want to center a 4X4 image with 2x2
pixel spacing aroung the position 0,0 as, I guess, you want to, then
the coordinate of the corner of your image should be -3,-3. You can
look at slide 19 of this presentation for a scheme:
www.cs.cmu.edu/~galeotti/methods_course/Lecture16-ITKImages.pptx
I hope this helps,
Simon

>
> Thanks very much!
>
> Patrick L. Liu
>
>
>
>
> On Wed, Jan 15, 2014 at 1:36 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
>>
>> Hi,
>> Thanks for the kind words Patrick. To complement Jan's answer:
>> - rtkparkershortscanweighting may be used to see the effect of the
>> Parker weighting,
>> - rtkfdk automatically triggers Parker weighting when it detects that
>> the scan is short. There is a threshold in the Parker implementation
>> for this, 20 degrees. See rtkParkerShortScanImageFilter.txx for more
>> details.
>> - you just have to add the option --arc to make the scan short, e.g.,
>> --arc=200. I have added a comment on the wiki about it:
>>  http://wiki.openrtk.org/index.php/RTK/Scripts/FDK
>> Simon
>>
>> On Wed, Jan 15, 2014 at 5:03 AM, Jan Hoskovec <jean.hoskovec at gmail.com>
>> wrote:
>> > Hello,
>> >
>> > rtkparkershortscanweighting is indeed for preprocessing the projection
>> > data. I don't think there is a tutorial for it, if none of the scripts
>> > mentioned on wiki.openrtk.org matches your case (you'd better re-check
>> > that).
>> >
>> > To generate a geometry file, you will need to run
>> > rtksimulatedgeometry. Typing "rtksimulatedgeometry -h" should provide
>> > enough information, but I suggest you read
>> > http://www.creatis.insa-lyon.fr/~srit/geometry.pdf should you be
>> > confused about the geometric conventions.
>> >
>> > The -p and -r options specify the input file(s). The tool is designed
>> > to be able to treat multiple files at the same time, so you specify
>> > the directory (-p) and a file name pattern (-r) separately. If you
>> > have just one file in your current working directory that you want to
>> > treat, then you can type "-p . -r <nameofthefile>". The -o option is
>> > quite straightforward, it's the name of the output image.
>> >
>> > Anyhow, all RTK command line binaries have a reasonably detailed help
>> > available if you launch them with the "-h" option.
>> >
>> > I hope these little hints will help you to find your way out. Don't
>> > worry, my first reconstruction with RTK was just about as chaotic.
>> >
>> > Regards,
>> >
>> > Jan
>> >
>> > 2014/1/15 Langechuan Liu <llgc at umich.edu>:
>> >> Hello,
>> >>
>> >> I am new to RTK. Thanks to the creators for building such a great
>> >> toolset.
>> >>
>> >> I found information about RTK because I was trying to perform a CBCT
>> >> recon
>> >> based on a short scan obtained from Varian OBI.
>> >>
>> >> In my specific case, I have 372 projection images (both in the original
>> >> Varian .hnd format, and raw projection format converted with
>> >> plastimatch)
>> >> scanned over 220 degrees of the phantom.
>> >>
>> >> I have followed the instructions on the wiki page and successfully
>> >> installed
>> >> RTK. However I could not find much documentation regarding the parker
>> >> short
>> >> scan weighting tool. I did find some prompts after typing into command
>> >> line:
>> >>
>> >> user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting
>> >> ./rtkparkershortscanweighting: '--geometry' ('-g') option required
>> >> ./rtkparkershortscanweighting: '--path' ('-p') option required
>> >> ./rtkparkershortscanweighting: '--regexp' ('-r') option required
>> >> ./rtkparkershortscanweighting: '--output' ('-o') option required
>> >>
>> >> Judging from the name, I suppose this rtkparkershortscanweighting tool
>> >> is to
>> >> preprocess the projection data, but I am not sure. I am also puzzled at
>> >> what
>> >> I should specify for each of the options, especially the geometry
>> >> option
>> >> (how should I generate the geometry file, etc). I googled but to no
>> >> avail.
>> >>
>> >>
>> >> Could somebody direct me to a tutorial, or shed some light on the usage
>> >> of
>> >> the command line tool?
>> >>
>> >> Thanks very much!
>> >>
>> >> Best Regards,
>> >> Patrick L. Liu
>> >>
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>> >>
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>
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