<div dir="ltr">Hi Simon,<div><br></div><div>The --proj_iso_x and --proj_iso_y arguments are confusing to me.</div><div><br></div><div>Their explanation states that they are the X/Y coordinates on the projection image of isocenter, but in practice I found them to be the projection offset in X/Y wrt to central ray (similar to --source_x and --source_y arguments).</div><div><br></div><div>Therefore in the above case I would give --proj_iso_x=-202.3 --proj_iso_y=-202.3 if the image origin is at pixel (0,0) and the +x and +y directions are aligned with the i and j indices of projection images, respectively, which is the normal case when reading from TIFF files.<br></div><div><br></div><div>In rtk::ThreeDCircularProjectionGeometry::AddProjectionInRadians() this two arguments are named as projOffsetX and projOffsetY, similar to the ones for the source sourceOffsetX and sourceOffsetY, implying that the argument description is problematic. The way of calculation of submatrix AddProjectionTranslationMatrix( ComputeTranslationHomogeneousMatrix(sourceOffsetX-projOffsetX, sourceOffsetY-projOffsetY) ) also supports that they are projection origin wrt isocenter instead of isocenter wrt projection origin.</div><div><br></div><div>Best regards,</div><div>Chao</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr">simon.rit@creatis.insa-lyon.fr</a>> 于2018年8月21日周二 下午1:26写道：<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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" target="_blank">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_1724504761894812058m_5471820206853289339gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><p style="margin-bottom:0.0001pt"><span lang="EN-US" style="color:rgb(31,73,125)"><span lang="EN-US" style="font-size:11pt;line-height:16.8667px;font-family:Calibri,sans-serif">__________________________________</span></span></p><p style="margin-bottom:0.0001pt"><span lang="EN-US" style="color:rgb(31,73,125)"><span lang="EN-US" style="font-size:11pt;line-height:16.8667px;font-family:Calibri,sans-serif">Andreas Gravgaard Andersen</span></span></p><div><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Department of Oncology, </span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Aarhus University Hospital<u></u><u></u></span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span lang="DA" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Nørrebrogade 44,</span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span lang="DA" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">8000, Aarhus C<u></u></span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span lang="DA" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Mail: <a href="mailto:agravgaard@protonmail.com" target="_blank">agravgaard@protonmail.com</a></span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><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)">+45 3165 8140</a></p></div></div></div></div></div></div></div></div><br></div></div><br><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">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_1724504761894812058m_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">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_1724504761894812058m_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">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)">+45 3165 8140</a></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</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">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">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">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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</blockquote>
</div>
</blockquote>
<br>
</div>
</blockquote></div>
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