Thank you! The very elegant solution did the trick! :-)
FYI I also tried -useitk 0 but it creates a vti only with one image instead of the stack. Probably I should specify the pattern instead of using -ifile, but I am having the problem with the file name pattern. Anyway, modifying the vti works fine! I have another question: is it possible to apply a transformation to a vti? The goal would be to display it in e.g. Paraview in the physical space, given by the MRI header. So I don't want to reslice it, just to basically rotate and translate it on the bases of a transformation matrix. Thanks! Lucia On Mar 2, 2012, at 8:48 AM, Luca Antiga wrote: > Hi Lucia, > the (admittedly obscure) reason why the spacing is ignored is that by default > vmtk uses the ITK I/O factories to read images, while some of the options > are used in case you use > -useitk 0 > This should fix it. > > On the other hand, you can (very elegantly) open the vti file with a text > editor, change the spacing and save :-) > > On my hand, I'll try to come up with a better way of enforcing the spacing > even when one uses the default -useitk 1 option. > > Best regards > > > Luca > > > On Mar 2, 2012, at 2:41 PM, Lucia Mirabella wrote: > >> Hi Luca, hi all, >> >> I'm trying to build a vti from a set of tiff images. Since the slice >> thickness is different from the in-plane resolution, I would like to set the >> correct spacing. I tried with >> >> vmtkimagereader -f tiff -ofile image_volume.vti -ifile Segmented_00.tiff >> -spacing 1.5625 1.5625 10 >> >> However image_volume.vti has the default spacing 1 1 1. >> >> I also tried using >> >> vmtkimagereader -f tiff -ofile image_volume.vti -d ./prova/ -spacing 1.5625 >> 1.5625 10 -prefix Segmented_ -pattern %s%02d.tiff >> >> but I get this error >> >> Reading TIFF image file. >> ERROR: In /Users/vmtk/tmp7/VTK/IO/vtkTIFFReader.cxx, line 324 >> vtkTIFFReader (0x7407aa0): Unable to open file Segmented_-1.tiff >> >> So apparently it's looking for a file with a dash (instead of a 0) before >> the number. >> >> Do you have an idea on what I am doing wrong? >> >> Thank you very much! >> >> Lucia >> >> >> __________________________________________________ >> >> Postdoctoral Fellow, Cardiovascular Fluid Mechanics Laboratory >> Wallace H. Coulter Department of Biomedical Engineering >> Georgia Institute of Technology >> 315 Ferst Drive NW, Parker H. Petit Biotechnology Building >> Atlanta, GA 30332-0363 >> E-mail: lucia.mirabe...@bme.gatech.edu >> >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> vmtk-users mailing list >> vmtk-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > __________________________________________________ Postdoctoral Fellow, Cardiovascular Fluid Mechanics Laboratory Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology 315 Ferst Drive NW, Parker H. Petit Biotechnology Building Atlanta, GA 30332-0363 E-mail: lucia.mirabe...@bme.gatech.edu ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ vmtk-users mailing list vmtk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users
