On 12.02.2013 10:47, Clarkson, Matt wrote: > Hi there, > > I have a 2 directories full of DICOM slices from a GE CT scanner. > > In the first folder I have 342 slices, that I would expect to be 3 volumes of > 114 slices. However, the data is read in as 115 volumes. One of those 115 > volumes has 114 slices. The remaining 114 volumes have 2 slices each.
> In the second folder I have 513 slices, that I would expect to be 3 volumes > of 117 slices. However, the data is read in as 2 volumes. Both have 117 > slices, but 1 volume as 2 time points, and the other volume has 1 time point. > > My "expected" number of slices comes from the fact that the scan protocol had > 3 phases for contrast enhancement and if I ask micron to convert to nifti I > get 3 volumes… which seems OK. Dear Matt, unfortunately you ran into a missing detail of our DICOM reading.. I just documented the missing feature in http://bugs.mitk.org/show_bug.cgi?id=14487 The short summary is: the reader needs to group files and does this by comparing UIDs/sizes/orientation/etc. In your case this is not enough to distinguish the three phases. From what I can see, "Acquisition Time" would be a good differentiator, but this cannot be generalized. What happens next is that each group of files is separated into 3D slice stacks with equal slice spacing. Unfortunately one of your stacks is shifted a bit and creates the impression (for the reader) that a very small inter-slice distance is correct. However, it cannot find more than two slices and starts creating new slice stacks, each of the size of 2. A proper fix would require us to first rethink how our GUI and reader work together, so it cannot be implemented as a quick bugfix. It does not help you much to know, but at least you have proved that there is demand for users to select proper interpretation. My suggestion is to work around this issue by separating the files into different folders and load them individually. OR, if this is a possibility for you, you could try to make your scanner output separate series for separate scans (with distinct UIDs). Regards, Daniel -- Dr. Daniel Maleike Telefon: + 49 6221 647976 3 Mint Medical GmbH, Friedrich-Ebert-Straße 2, 69221 Dossenheim/Heidelberg Geschäftsführer: Dr. Matthias Baumhauer Registergericht Mannheim, HRB 709351 ------------------------------------------------------------------------------ Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
