<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">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="gmail_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 Sun, 19 Aug 2018 at 23:44, Milan Manasijevic <<a href="mailto:milan-manasijevic@t-online.de">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>