Clarkson, Matt <m.clarkson@...> writes: > > Great! Thanks for this. > It's on my radar for next week ... hopefully. > Matt > > On 11 Jul 2012, at 21:18, Senseney, Justin (NIH/CIT) [E] wrote: > > > Just to provide a data point you might find useful, I have encountered 3D/4D data in one file on a more > regular basis in the past year. First, with Siemens mosaic data from a diffusion weighted study. These > typically need a separate step to converting them into a standard serial image set with conforming DICOM > tags. More common now is "enhanced" DICOM (but again I typically only encounter these in MR). The relevant > tags are (0020, 9057), and others found within sequence (0020,9222) discussed in C.7.6.16.2.2.4 of PS3 > of the DICOM standard. For MR, you can see supplement 49: > ftp://medical.nema.org/medical/dicom/final/sup49_ft.pdf. Outside of MR, the use of these can be > found on page 452 of this document: http://medical.nema.org/Dicom/2011/11_03pu.pdf. > > > > These do have the potential to save quite a bit of space, as only the first frame contains the repeating tags > of all other image slices in that frame. > > > > Enjoy, > > Justin Senseney > > BIRSS/ISL/DCB/CIT/NIH > > Building 12A/2015 > > http://dcb.cit.nih.gov/~senseneyj > > http://mipav.cit.nih.gov > > > > > > > > -----Original Message----- > > From: Clarkson, Matt [mailto:m.clarkson@...] > > Sent: Wednesday, July 11, 2012 3:06 AM > > To: Graser, Bastian > > Cc: mitk-users > > Subject: Re: [mitk-users] DICOM : 3D data in one file. > > > > Hi Bastian, > > > > Thats pretty much what I was thinking of implementing. I will give it a go. > > Thanks > > > > M > > > > On 10 Jul 2012, at 11:01, Graser, Bastian wrote: > > > >> Hi Matt, > >> > >> Afaik there is no statement in the dicom standard for having a 3D/4D volume in a single DCM file. Still you > sometimes encounter such files. So far we only encountered them when exporting 3D/4D ultrasound data > from Philips QLab software. For these, we wrote a special procedure to read them. So, we only support these yet. > >> > >> If you have a similar special case of DCM data, you might need to add > >> another extra procedure to handle these. You can do it pretty much the > >> same way as it is done for Philips3D Ultrasound data. (see > >> DicomSeriesReader::ReadPhilips3DDicom in mitkDicomSeriesReader.cpp) > >> > >> 1.) In the method DicomSeriesReader::LoadDicom in mitkDicomSeriesReader.txx perform a check to > identify, if the present dcm is of your special kind. There are propably meta tags&values for your special > dcm format, which you can check for. > >> 2.) if so, call a read-function for your special dcm, which should be > >> implemented in DicomSeriesReader::ReadMatts3DDicom(..). Again, just copy&paste&adapt the > ReadPhilips3DDicom function. > >> > >> Biggest task here is to figure out, which tags are used for all the geometry information you need (spacing > x, y, z, rotation, timesteps,..) since they are probably put into user-defined tags. You can use some > external program like DCMTK's dcmdump or Dicom Inspector.Net to have a look at all tags. If you send me a > list of all the tags and their value in your file, I might have a look. But please delete personal > information first (name, bday) if existing. Keep in mind that due to the nature of some images, geometry > data might be missing (e.g Philips 3D ultrasound data does not have an origin). In that case, fill in > standard values (Origin = 0,0,0; Spacing= 1,1,1; Rotation = 1, 0, 0 ,1). Another challenge is to find out, > in what order the data is stored, so you can read it correctly out of the data-Tag. This is a little trial & > error. > >> > >> > >> Regards, > >> Bastian > >> > >> -----Ursprüngliche Nachricht----- > >> Von: Clarkson, Matt [mailto:m.clarkson@...] > >> Gesendet: Mittwoch, 20. Juni 2012 10:15 > >> An: mitk-users > >> Betreff: [mitk-users] DICOM : 3D data in one file. > >> > >> Hi there, > >> > >> with regard to my previous questions here: > >> http://sourceforge.net/mailarchive/forum.php?thread_name=ECE4A32F-30FC > >> -4B09-9189-1671B767274D%40live.ucl.ac.uk&forum_name=mitk-users > >> > >> issues 3 and 4 were not caused by tag 0020,0037 (orientation), or tag 0020,0032 (patient position) being > missing. The data was in fact SPECT data, where the complete 3D volume is contained within one .dcm file. > >> So, does MITK support this? I have only seen a special case for Philips 3D ultrasound. > >> Has anyone else had a similar problem and resolved it? > >> Any suggestions on how it should be resolved? > >> > >> Thanks as always. > >> > >> Matt > >> > >> > >> > >> ---------------------------------------------------------------------- > >> -------- > >> 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. > >> Discussions will include endpoint security, mobile security and the > >> latest in malware threats. > >> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > >> _______________________________________________ > >> mitk-users mailing list > >> mitk-users@... > >> https://lists.sourceforge.net/lists/listinfo/mitk-users > >> > > > > > > > > ------------------------------------------------------------------------------ > > 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. Discussions will include endpoint security, mobile security and the latest in > malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > _______________________________________________ > > mitk-users mailing list > > mitk-users@... > > https://lists.sourceforge.net/lists/listinfo/mitk-users > > > > ------------------------------------------------------------------------------ > > 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. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > _______________________________________________ > > mitk-users mailing list > > mitk-users@... > > https://lists.sourceforge.net/lists/listinfo/mitk-users > > > > ------------------------------------------------------------------------------ > 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. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >
All, I currently have Philips Ultrasound 3D dicoms that I need to work with. Unfortunately, I am not able to get MITK to correctly import and display the volume data; it is displayed as a single image. If you could provide some guidance on the technique stated above on how this Philips data was imported, I would greatly appreciate it. Thank you. Charles ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
