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Hi luis,<br>
<br>
Thanks for your advices to register my volumes.<br>
<br>
1-2) I work with volview, so I can crop volumes but the only format I
can save for future use is .raw . Volview don't generate a header file
for raw datas. That's the reason why I didn't know the*.mha files. Now,
I'll edit the *.mha files!<br>
I use the itkRegionOfInterestImageFilter, and that's great!<br>
File format isn't a problem anymore.<br>
<br>
3)I don't know how to rescale intensity. PET images are very dark
(pelvis images). Since there's no visible anatomical structures, I'm
wondering if it is possible to register that type of volumes. I tried
to lighten the volume with shiftfilter plus rescaleintensityfilter but
the result isn't very satisfactory. I will try with
IntensityWindowingImageFilter.<br>
I had some results but have still some questions:<br>
What is the resulting volume of MultiResMIRegistration filter? It seems
to be the moving volume on which is applied the rigid transform (and
rescale) computed by the filter .<br>
How can I see the registration result? Is there any filter which merges volumes or overlays slices one by one?<br>
<br>
4) I read a lot of publications about mutual information to know how it
works and know more about filter parameters of
MultiResMIRegistrationfilter.<br>
<br>
Thanks,<br>
<br>
Laurent.<br>
<br>
<br>
<br>----Message d'origine----
<br>>Date: Sat, 02 Apr 2005 11:15:20 -0500
<br>>De: Luis Ibanez <luis.ibanez @kitware.com="">
<br>>A: laurent.paul@club-internet.fr
<br>>Copie à: insight-users@itk.org
<br>>Sujet: Re: [Insight-users] MultiResMIRegistration problem
<br>>
<br>>
<br>>
<br>>Hi Laurent,
<br>>
<br>>
<br>> Coffee always helps !!
<br>>
<br>>
<br>>Here are some things that you may want to do before passing
<br>>your images to the MultiResMIRegistration program:
<br>>
<br>>1) Convert your DICOM series to a format that uses a single
<br>> image. You can do this with the programs in
<br>>
<br>>
<br>> Insight/Examples/IO/
<br>> DicomSeriesReadImageWrite.cxx
<br>> DicomSeriesReadImageWrite2.cxx
<br>>
<br>> or with the GUI applicaition MRIConvert
<br>>
<br>> http://lcni.uoregon.edu/~jolinda/MRIConvert
<br>>
<br>>
<br>>
<br>>2) You must crop the CT image in order to contain only the
<br>> region that will match the PET image. This will save
<br>> *a lot* of computing time, and will prevent the registration
<br>> from falling into false positive matchings.
<br>>
<br>>
<br>>3) You should rescale the intensities of the CT and the PET
<br>> in order to highlight the structures that you expect to
<br>> be matched. For example, body contours. This is important
<br>> because Mutual Information uses a joint histogram that covers
<br>> the entire dynamic range of each image. If structures that
<br>> are supposed to match between the PET and CT images are
<br>> restricted to a small region of intensities in the histogram
<br>> then the Mutual Information metric will be less sensitive to
<br>> the 'goodness' of the matching.
<br>>
<br>> You can use the filters:
<br>>
<br>> RescaleIntensityImageFilter
<br>> IntensityWindowingImageFilter
<br>>
<br>> for that purpose.
<br>> You want to make sure that after this filters, you images
<br>> only have intensities in the range of the anatomical structures
<br>> that are visible both in the CT and PET images simultaneously.
<br>>
<br>>
<br>>
<br>>4) You should read the documentation of this application:
<br>>
<br>> InsightApplications/
<br>> MultiResMIRegistration/
<br>> ReadMe.doc
<br>> ReadMe.pdf
<br>>
<br>>
<br>>
<br>>5) You can also try the application
<br>>
<br>> InsightApplications/
<br>> LandmarkInitializedMutualInformationRegistration
<br>>
<br>> (if you don't feel like building it, you can download
<br>> the binary version from the UNC CADDLab web site)
<br>>
<br>> http://caddlab.rad.unc.edu/software/
<br>>http://caddlab.rad.unc.edu/software/request.php?file=3DRegistrationTool/3DRegistrationTool_win.zip
<br>>
<br>>
<br>>
<br>>Please let us know if you still have any questions,
<br>>
<br>>
<br>> Thanks
<br>>
<br>>
<br>>
<br>>
<br>> Luis
<br>>
<br>>
<br>>
<br>>
<br>>-------------------------------------
<br>>laurent.paul@club-internet.fr wrote:
<br>>
<br>>>
<br>>> Hi!
<br>>>
<br>>> I need help! Take a cup of columbian coffee!
<br>>> I try to use MultiResMIRegistration example.
<br>>>
<br>>> To be simple, I have series of Dicom files for CT and Analyze for PET. I
<br>>> can convert these in any type of file (except ones I don't know as .mha
<br>>> .mhd). I'd want to register these series.
<br>>> It would be great if you could say me what type of volume I can use
<br>>> (Analyze, serie of 2D images as TIFF, JPG, PNG, Dicom, or other).
<br>>> Apparently, the volume is passed by his header file?
<br>>> Is the two volumes must have the same dimensions (number of slices) and
<br>>> include the same part of the volume? In fact PET embodies the whole
<br>>> patient when the CT embodies only the pelvis. Is that a problem?
<br>>>
<br>>> I saw in users archives that I could use *.mha files. What are that
<br>>> files? I have some but can't open them. Tell me more about that format.
<br>>> Softwares tell me header is wrong(?!).
<br>>>
<br>>> I managed to run the application but just for 2D file. The result is
<br>>> very bad but that's normal becuse the files I tried to register are
<br>>> pelvis images (PET contains few informations, just the tumor). I'd want
<br>>> to try before with brain images (less difficult to register I think). I
<br>>> saw in the users archives that there are images on the ftp server,
<br>>> brainweb165a10f17 and brainweb1e5a10f17Rot10Tx15. I didn't find them. Is
<br>>> this application works with 2D images?
<br>>>
<br>>> Least, I don't understand some parameters.
<br>>> Line 5: Multi resolution level? Which level?
<br>>> Line 6-7:starting level?
<br>>> Line 10: Scale applied?
<br>>>
<br>>> I know that's a lot of questions but I don't understand Please, just
<br>>> give me some keys to register brain images.
<br>>>
<br>>> Thanks for your help.
<br>>>
<br>>> Laurent PAUL.
<br>>>
<br>>>
<br>>> ------------------------------------------------------------------------
<br>>>
<br>>> _______________________________________________
<br>>> Insight-users mailing list
<br>>> Insight-users@itk.org
<br>>> http://www.itk.org/mailman/listinfo/insight-users
<br>>
<br>>
<br>>
<br>>
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