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Hi Simon,<br>
<br>
my understanding of origin in this context was wrong. Your advise
makes sense and I ran the reconstruction succesfully by setting the
values --proj_iso_x=-202.3 --proj_iso_y=-202.3. I didn't investigate
the result further, but at first glance it is a big step ahead for
me. Regarding the source_y value, It is given in the test.pca and
also in the test.pcj file (please check the dropbox). <br>
Similar to the value of the ZSample=180.611687 (which is SID) the
value of YSample is given by YSample=-16.412937. My understanding is
that this should be the SourceOfsetY. However, in my first attempt
today, I didn't use that argument. <br>
<br>
Many thanks for helping me.<br>
<br>
Best Regards,<br>
Milan<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 21.08.2018 um 13:25 schrieb Simon
Rit:<br>
</div>
<blockquote type="cite"
cite="mid:CAF0oig2KnfcxtY+7sYQnj6yEXgtH763nuWmMSrehrOXO+Msm_A@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<div dir="ltr">
<div>Hi,</div>
<div>It's not clear to me how you came up with your source_y
value. Assuming that the origin of your projections is 0,0,0,
I would advise to set the geometry with --proj_iso_x=202.3
--proj_iso_y=202.3 (or, equivalently, set a new origin to the
projection equal to -202.3,-202.3,0).</div>
<div>The --arc value is also a bit surprising but you can check
if the assigned GantryAngle is the correct one for each
projection.</div>
<div>Finally, in rtkfdk, setting origin (this time for the
volume) to a y-value equal 0 means that you only look at the
part above the source trajectory. I would leave the default
values (centered volume around the center of rotation).</div>
<div>Best regards,<br>
</div>
<div>Simon<br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Tue, Aug 21, 2018 at 12:01 AM Andreas Andersen
<<a href="mailto:andreasga22@gmail.com"
moz-do-not-send="true">andreasga22@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Milan
<div><br>
</div>
<div>1) OK, I guess it makes sense with the source/detector
geometry.</div>
<div><br>
</div>
<div>2) I forgot to check which group RawImageIO was in;
it's own apparently.</div>
<div>So you'll have to re-compile ITK with the CMake option:
Module_ITKIORAW=ON<br>
(You'll have to add the entry manually if you use a CMake
GUI)</div>
<div><br>
</div>
<div>3) Origin is not the isocenter, it is the offset of the
image origin, i.e. index 0,0,0, in relation to the
isocenter (AFAIK). </div>
<div>Just a guess: Try with an offset of: -0.03840368 *
{421,0,471} / 2 => "--origin -8.08,0,-9.04"<br>
(I forget the definition of the y-axis, so I'm unsure
about the "0", if it doesn't work also try -10.23, 10.23,
multiplying it by 2, and 0.)</div>
<div><br>
</div>
<div>Best regards</div>
<div>Andreas<br clear="all">
<div>
<div dir="ltr"
class="m_5471820206853289339gmail_signature">
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<div class="gmail_quote">
<div dir="ltr">On Mon, 20 Aug 2018 at 22:10, Milan
Manasijevic <<a
href="mailto:milan-manasijevic@t-online.de"
target="_blank" moz-do-not-send="true">milan-manasijevic@t-online.de</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi Andreas,<br>
I am really grateful that you've found time to response
so quickly.<br>
<br>
1) Following your suggestions I first checked the
spacing. I suppose, you refer to the value of
0.03840368. I am confident, this is the correct value in
the correct unit (mm). <br>
The 4D Slicer shows the dimensions in mm and this is
near to the object measures.<br>
<br>
2) The second try was to check if the " -o fdk.raw"
works. <br>
Unfortunately not, I get such exception:<br>
itk::ImageFileWriterException (000000C71D4FE5D0)<br>
Location: "void __cdecl itk::ImageFileWriter<class
itk::Image<float,3> >::Write(void)"<br>
File:
d:\reconstruction_rtk\itk\modules\io\imagebase\include\itkImageFileWriter.hxx<br>
Line: 151<br>
Description: Could not create IO object for writing
file fdk.raw<br>
Tried to create one of the following:<br>
NiftiImageIO<br>
NrrdImageIO<br>
GiplImageIO<br>
HDF5ImageIO<br>
JPEGImageIO<br>
BMPImageIO<br>
LSMImageIO<br>
PNGImageIO<br>
TIFFImageIO<br>
VTKImageIO<br>
StimulateImageIO<br>
BioRadImageIO<br>
MetaImageIO<br>
MRCImageIO<br>
GE4ImageIO<br>
GE5ImageIO<br>
HndImageIO<br>
XimImageIO<br>
HisImageIO<br>
ImagXImageIO<br>
DCMImagXImageIO<br>
EdfImageIO<br>
XRadImageIO<br>
OraImageIO<br>
GDCMImageIO<br>
You probably failed to set a file suffix, or<br>
set the suffix to an unsupported type.<br>
<br>
<br>
3) Regarding the "--origin argument" and refering to my
context (see attached files please), what would you
suggest, what should I pass as the origin values? The
detecetor origin is at 0,0 but for the Volume I am not
quit sure if I should provide some values and which
(actually isocenter should be at 0,0,0 and if I provide
these values I still get no result ). Probably this
would solve my problem. <br>
<br>
Again, many thanks for your time and thank you for your
help.<br>
<br>
Best regards,<br>
Milan<br>
<br>
<br>
<br>
<br>
<div
class="m_5471820206853289339m_-13397226491706609moz-cite-prefix">Am
20.08.2018 um 14:26 schrieb Andreas Andersen:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Milan
<div><br>
</div>
<div>I didn't open the dropbox link, but I think in
general one should take an extra look at the
rtkfdk arguments if nothing "meaningful" comes
out:</div>
Is your spacing in the correct unit (mm)? it seems
quite small in relation to the dimensions.
<div> Also try adding the --origin argument.</div>
<div><br>
</div>
<div>Additional 1:</div>
<div>Slicer is a good tool for exactly that. </div>
<div>( I have also made a similar tool with some
reconstruction options, mainly for scatter
correction: <a
href="https://gitlab.com/agravgaard/cbctrecon/wikis/Installation"
target="_blank" moz-do-not-send="true">cbctrecon</a> )</div>
<div>Additional 2:</div>
<div>try giving " -o fdk.raw" instead of "-o
fdk.mha", the default output value type is 32-bit
floating point.</div>
<div><br>
</div>
<div>Best regards</div>
<div> Andreas</div>
<div>
<div>
<div dir="ltr"
class="m_5471820206853289339m_-13397226491706609gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<p style="margin-bottom:0.0001pt"><span
style="color:rgb(31,73,125)"
lang="EN-US"><span
style="font-size:11pt;line-height:16.8667px;font-family:Calibri,sans-serif"
lang="EN-US">__________________________________</span></span></p>
<p style="margin-bottom:0.0001pt"><span
style="color:rgb(31,73,125)"
lang="EN-US"><span
style="font-size:11pt;line-height:16.8667px;font-family:Calibri,sans-serif"
lang="EN-US">Andreas Gravgaard
Andersen</span></span></p>
<div>
<p><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Department
of Oncology, </span></p>
<p><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Aarhus
University Hospital</span></p>
<p><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"
lang="DA">Nørrebrogade 44,</span></p>
<p><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"
lang="DA">8000, Aarhus C</span></p>
<p><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"
lang="DA">Mail: <a
href="mailto:agravgaard@protonmail.com"
target="_blank"
moz-do-not-send="true">agravgaard@protonmail.com</a></span></p>
<p><span
style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt">Cell: </span><span
style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt"> </span><a
value="+4523382411"
style="font-family:Calibri,sans-serif;font-size:11pt;color:rgb(17,85,204)"
moz-do-not-send="true">+45
3165 8140</a></p>
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</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Sun, 19 Aug 2018 at 23:44, Milan
Manasijevic <<a
href="mailto:milan-manasijevic@t-online.de"
target="_blank" moz-do-not-send="true">milan-manasijevic@t-online.de</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi
RTK-users,<br>
<br>
I am trying to reconstruct a sample scanned using
the CBCT. Rtk seems to <br>
be the best chioce for that, but unfortenately I
have no success.<br>
Hopefully, some of you guys can help.<br>
<br>
The outcome of the scanning are 2500 projections
(each 2024x2024 pixels).<br>
The increasement of the rotation angle is 0.144
degree<br>
To reduce the reconstruction time I use just 79
projection images and <br>
angle increasement is 4.608 degree.<br>
<br>
The data regarding the scanning process are
(test.pca, test.pcj and <br>
test.pcr) dropped <br>
here:<a
href="https://www.dropbox.com/sh/on7c049aqx5ep1r/AAA7THDCkIHPF_9DBRl7MwROa?dl=0"
rel="noreferrer" target="_blank"
moz-do-not-send="true">https://www.dropbox.com/sh/on7c049aqx5ep1r/AAA7THDCkIHPF_9DBRl7MwROa?dl=0</a><br>
<br>
From these three files I have the following
values required for the <br>
reconstruction:<br>
[Geometry]<br>
FDD=940.59570922<br>
FOD=180.61168750<br>
VoxelSizeX=0.03840368<br>
VoxelSizeY=0.03840368<br>
<br>
[VolumeData]<br>
Volume_SizeX=421<br>
Volume_SizeY=533<br>
Volume_SizeZ=471<br>
<br>
[Detector]<br>
PixelsizeX=0.20000000<br>
PixelsizeY=0.20000000<br>
NrPixelsX=2024<br>
NrPixelsY=2024<br>
<br>
Finally, these are commands that I used to
reconstruct the volume:<br>
<br>
==========================================================================================================================================<br>
rtksimulatedgeometry --output="geometry.xml"
--nproj=79 --arc=364.032 <br>
--sdd=940.59570922 --sid=180.611687
--source_y=-16.412937<br>
rtkprojections --path "d:\data\test\tiffs"
--output "projections.mha" <br>
--regexp .tif --newspacing 0.2<br>
rtkfdk -p . -r projections.mha -o fdk.mha -g
geometry.xml <br>
--spacing=0.03840368,0.03840368,0.03840368
--dimension=421,533,471<br>
==========================================================================================================================================<br>
<br>
I use the VV, the 4D Slicer to check the results
fro both, <br>
projections.mha and fdk.mha. The first one looks
fine and shows tha <br>
sample correctly, but fdk.mha does not show any
meaningfull information.<br>
The jpgs that show that, you can also find in the
dropbox.<br>
<br>
Probably, I need to include the ROI values given
in the test.pcr file <br>
but I am not sure how. Would that be the neworigin
value. (I have tried <br>
but no success).<br>
<br>
Any help on that is highly appreciated!<br>
<br>
<br>
In addition I would have another two questions:<br>
1. Can anyone advice a proper tool to check the
reconstruction result <br>
(the reconstructed volume)?<br>
2. I am using the Voreen (<a
href="https://www.uni-muenster.de/Voreen/"
rel="noreferrer" target="_blank"
moz-do-not-send="true">https://www.uni-muenster.de/Voreen/</a>)
and would <br>
rather have the reconstruction result in a raw
file format (containing <br>
intensities as a 32-Bit floats). How can I convert
mha into raw? (I <br>
tried to split the mha into mhd and raw, but no
success)<br>
<br>
Best Regards,<br>
Milan<br>
<br>
<br>
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