Hi Luca, When I tried using vmtkimagereader -ifile /Image_path/IM000000.dcm I got the error "Archetype file /Image_path/IM000000.dcm does not exist". I tried copying and pasting the dicom files to several different directories and this error still persists. I also tried vmtkimagereader -ifile /Image_path/IM000000 (with the .dcm file extension) and I at least don't get the error but the resulting models are still mis-aligned. What am I overlooking?
Thanks for all the help! Anna ________________________________________ From: Luca Antiga [luca.ant...@orobix.com] Sent: Wednesday, July 18, 2012 11:01 AM To: Hoppe, Anna L Cc: vmtk-users@lists.sourceforge.net Subject: Re: [vmtk-users] vmtk spatial location question Hi Anna, yes, please try the -ifile way. It should work. Best, Luca On Jul 18, 2012, at 4:26 PM, Hoppe, Anna L wrote: > > Hi Luca, > > ok. I'm glad to know that vmtk & Slicer rely on the same code for position > estimation. > > To initially segment the image sets I used vmtkimagereader -f dicom -d > dicom_directory. Do you think I should try vmtkimagereader -ifile > first_dicom_file_in_series.dcm instead? > > Thanks for all the help! > Anna > ________________________________________ > From: Luca Antiga [luca.ant...@orobix.com] > Sent: Wednesday, July 18, 2012 4:44 AM > To: Hoppe, Anna L > Cc: vmtk-users@lists.sourceforge.net > Subject: Re: [vmtk-users] vmtk spatial location question > > Hi Anna, > if Slicer loads the images right, then I'd expect vmtk to do the same since > they rely on the same code for estimating positioning and directions. > There must be something we're still missing from the picture. > > Quick question: how did you load the DICOM images initially, when you > segmented them? Using vmtkimagereader -f dicom -d your_directory (old way > that I should deprecate) or vmtkimagereader -ifile > first_dicom_file_in_series.dcm ? > > Thanks > > Luca > > > > On Jul 16, 2012, at 7:12 PM, Hoppe, Anna L wrote: > >> Hi Luca, >> >> I tried out the sequence of vmtk scripts you mentioned (vmtkimagereader >> -ifile 0001_0001.dcm --pipe vmtksurfacetransformtoras -ifile >> segmented_surface.vtp -ofile transformed_segmented_surface.vtp). The >> resulting transformed surfaces were still misaligned. After looking at the >> dicom header files for each volumetric dataset, there is a coordinate >> position archived under the name "Image position (patient)" that differs in >> the two datasets, I think that this may be what you referred to as the >> "patient's coordinate space"; however, when I load these same two image sets >> in 3DSlicer and generate surface models within this program these models >> are aligned perfectly. So, I know that the two image sets share the same >> physical coordinate space, it's just that the two only partially overlap >> within that same physical space (with the overlapping region being what I'm >> interested in). 3DSlicer is apparently using some info. from each dicom >> header file in order to generate aligned surfaces, I'm just not sure what >> info. (after having parsed the header and taking a look at the archived data >> within -- there doesn't seem to be any image location coordinates other than >> the "image location (patient)" archive?). So I am wondering if it's >> possible, assuming I find out some info. about the physical coordinate >> system my datasets share, to pass this info. onto vmtksurfaceviewer, or >> would a program like 3DSlicer be my only option for model generation for now? >> >> Thanks for your help. It is greatly appreciated. >> Anna >> ________________________________________ >> From: Luca Antiga [luca.ant...@orobix.com] >> Sent: Saturday, July 14, 2012 9:03 AM >> To: Hoppe, Anna L >> Cc: vmtk-users@lists.sourceforge.net >> Subject: Re: [vmtk-users] vmtk spatial location question >> >> Dear Anna, >> >> vmtk doesn't natively take into account image orientation yet. It has been >> in the wishlist for some time now, but it would require quite some work, >> hopefully I'll be able to get it done if there's enough interest in it. >> >> For the time being, you can recover the original orientation by transforming >> the segmented surfaces to their respective patient's coordinate space: >> >> vmtkimagereader -ifile 0001_0001.dcm --pipe vmtksurfacetransformtoras -ifile >> segmented_surface.vtp -ofile transformed_segmented_surface.vtp >> >> Note that you have to start from your original dicom series in the >> vmtkimagereader, since the transform matrix is taken from there. >> >> You should do this for both surfaces, and they should align at the end *if* >> the two patient reference frames where the same (which doesn't depend >> on vmtk, of course). >> >> If they aren't (you can load the images up in, say, Osirix, and check if the >> two series overlap), then you'll have to perform image registration first. >> To this end you could use 3DSlicer, it incorporates quite a few registration >> algorithms. >> >> Hope this helps. >> >> >> Luca >> >> >> >> >> On Jul 12, 2012, at 9:34 PM, Hoppe, Anna L wrote: >> >>> Hi VMTK users, >>> >>> I have two volumetric image sets taken at the same time point with slightly >>> different patient locations (according to the dicom header files). One is a >>> bone scan and the other is a contrast-enhanced vessel scan. When loading >>> these two data sets using vmtkimageviewer, vmtk assumes that they share the >>> same patient position and therefore share the same origin. Consequently >>> when the vessel and bone scans are segmented, they are clearly misaligned. >>> Does vmtk assume the same patient position when overlaying any two image >>> sets (the sets share the same number of pixel rows and columns and number >>> of images (512x512x512); additionally, they have the same pixel spacing)? >>> Is there a way to explicitly give vmtkimagereader the patient position of >>> each image set, so that the corresponding segmentations will be aligned? >>> >>> Thank you for your help, >>> Anna >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. 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