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<br>
Hi!<br>
<br>
That's ok, I managed to register PET and CT, and PET and MRI. I merged
the resulting and the fixed volumes, and I have a good result knowing I
don't vary the parameters.<br>
The merging volume is a bit dark, but I can do something with windowingfilter.<br>
<br>
ITK software guide is my bible! <br>
<br>
Thanks a lot!<br>
<br>
Regards,<br>
<br>
Laurent.<br>
<br>
<br>
<br>----Message d'origine----
<br>>Date: Wed, 06 Apr 2005 12:21:23 -0400
<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>>Hi Laurent,
<br>>
<br>>
<br>>1-2) Thanks for letting us know that you managed to read the images.
<br>> Note that VolView *does* create headers for RAW files. Those
<br>> headers are small files with extension .vvi. If you open a raw
<br>> file VolView will create one of these headers in the same location
<br>> of your .raw file. This header will be used if you read the raw
<br>> image a second time.
<br>>
<br>>3) Rescaling the intensity of the PET image is very important.
<br>> You may want to play with the Intensity Windowing controls on
<br>> VolView (or any other visualization program) in order to find
<br>> a range that will show you anatomical features. This is usually
<br>> in the very low range of PET intensities. Once you find a range
<br>> you can use the IntensityWindowingImageFilter in order to prepare
<br>> your image.
<br>>
<br>>
<br>>
<br>> The output of the MultiResMIRegistration program (and any other
<br>> ITK registration program for that matter) is the resampled moving
<br>> image using the final transform produced by the registration.
<br>> You *MUST* read the registration chapter from the ITK software guide
<br>> as well as the chapter on image resampling from the same document
<br>>
<br>> http://www.itk.org/ItkSoftwareGuide.pdf
<br>>
<br>>
<br>> You can compare the fixed image and resampled moving image by
<br>> merging them in VolView. Simply use the Merge plugin in the
<br>> Utility group of the Filters menu.
<br>>
<br>>
<br>>
<br>>
<br>> Regards,
<br>>
<br>>
<br>> Luis
<br>>
<br>>
<br>>
<br>>-------------------------------------------------
<br>>laurent.paul@club-internet.fr wrote:
<br>>
<br>>>
<br>>>
<br>>> 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
<br>>> can save for future use is .raw . Volview don't generate a header file
<br>>> for raw datas. That's the reason why I didn't know the*.mha files. Now,
<br>>> 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
<br>>> (pelvis images). Since there's no visible anatomical structures, I'm
<br>>> wondering if it is possible to register that type of volumes. I tried to
<br>>> lighten the volume with shiftfilter plus rescaleintensityfilter but the
<br>>> result isn't very satisfactory. I will try with
<br>>> IntensityWindowingImageFilter.
<br>>> I had some results but have still some questions:
<br>>> What is the resulting volume of MultiResMIRegistration filter? It seems
<br>>> to be the moving volume on which is applied the rigid transform (and
<br>>> rescale) computed by the filter .
<br>>> How can I see the registration result? Is there any filter which merges
<br>>> volumes or overlays slices one by one?
<br>>>
<br>>> 4) I read a lot of publications about mutual information to know how it
<br>>> 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
<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
<br>>> 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
<br>>> 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>>> >> _______________________________________________
<br>>> >> Insight-users mailing list
<br>>> >> Insight-users@itk.org
<br>>> >> http://www.itk.org/mailman/listinfo/insight-users
<br>>> >
<br>>> >
<br>>> >
<br>>> >
<br>>
<br>>
<br>>
<br>>
</luis.ibanez></body></html>