[Insight-users] MultiResMIRegistration problem

[Luis Ibanez]

Hi Laurent,


      Coffee always helps !!


Here are some things that you may want to do before passing
your images to the MultiResMIRegistration program:

1) Convert your DICOM series to a format that uses a single
    image. You can do this with the programs in


        Insight/Examples/IO/
           DicomSeriesReadImageWrite.cxx
           DicomSeriesReadImageWrite2.cxx

    or with the GUI applicaition MRIConvert

        http://lcni.uoregon.edu/~jolinda/MRIConvert



2) You must crop the CT image in order to contain only the
    region that will match the PET image. This will save
    *a lot* of computing time, and will prevent the registration
    from falling into false positive matchings.


3) You should rescale the intensities of the CT and the PET
    in order to highlight the structures that you expect to
    be matched. For example, body contours.  This is important
    because Mutual Information uses a joint histogram that covers
    the entire dynamic range of each image. If structures that
    are supposed to match between the PET and CT images are
    restricted to a small region of intensities in the histogram
    then the Mutual Information metric will be less sensitive to
    the 'goodness' of the matching.

    You can use the filters:

           RescaleIntensityImageFilter
           IntensityWindowingImageFilter

    for that purpose.
    You want to make sure that after this filters, you images
    only have intensities in the range of the anatomical structures
    that are visible both in the CT and PET images simultaneously.



4) You should read the documentation of this application:

        InsightApplications/
                 MultiResMIRegistration/
                                 ReadMe.doc
                                 ReadMe.pdf



5) You can also try the application

       InsightApplications/
         LandmarkInitializedMutualInformationRegistration

    (if you don't feel like building it, you can download
     the binary version from the UNC CADDLab web site)

           http://caddlab.rad.unc.edu/software/
http://caddlab.rad.unc.edu/software/request.php?file=3DRegistrationTool/3DRegistrationTool_win.zip



Please let us know if you still have any questions,


    Thanks




       Luis




-------------------------------------
laurent.paul at club-internet.fr wrote:

> 
> Hi!
> 
> I need help! Take a cup of columbian coffee!
> I try to use MultiResMIRegistration example.
> 
> To be simple, I have series of Dicom files for CT and Analyze for PET. I 
> can convert these in any type of file (except ones I don't know as .mha 
> .mhd). I'd want to register these series.
> It would be great if you could say me what type of volume I can use 
> (Analyze, serie of 2D images as TIFF, JPG, PNG, Dicom, or other). 
> Apparently, the volume is passed by his header file?
> Is the two volumes must have the same dimensions (number of slices) and 
> include the same part of the volume? In fact PET embodies the whole 
> patient when the CT embodies only the pelvis. Is that a problem?
> 
> I saw in users archives that I could use *.mha files. What are that 
> files? I have some but can't open them. Tell me more about that format. 
> Softwares tell me header is wrong(?!).
> 
> I managed to run the application but just for 2D file. The result is 
> very bad but that's normal becuse the files I tried to register are 
> pelvis images (PET contains few informations, just the tumor). I'd want 
> to try before with brain images (less difficult to register I think). I 
> saw in the users archives that there are images on the ftp server, 
> brainweb165a10f17 and brainweb1e5a10f17Rot10Tx15. I didn't find them. Is 
> this application works with 2D images?
>  
> Least, I don't understand some parameters.
> Line 5: Multi resolution level? Which level?
> Line 6-7:starting level?
> Line 10: Scale applied?
> 
> I know that's a lot of questions but I don't understand Please, just 
> give me some keys to register brain images.
> 
> Thanks for your help.
> 
> Laurent PAUL.
> 
> 
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