[Insight-users] Re: Insight-users Digest, Vol 16, Issue 75

Thu Sep 1 19:17:18 EDT 2005

Thanks


Xuelin
----- Original Message ----- 
From: <insight-users-request at itk.org>
To: <insight-users at itk.org>
Sent: Wednesday, August 31, 2005 3:41 PM
Subject: Insight-users Digest, Vol 16, Issue 75


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> Today's Topics:
>
>   1. registration pipeline suggestion (rvivanco at cs.umanitoba.ca)
>   2. Help creating a element in  ITK FEM  (Barbara Garita)
>   3. Re: registration pipeline suggestion (Luis Ibanez)
>   4. RE: Local smoothing of a deformation field
>      (Miller, James V (Research))
>   5. Histogram stretch (Yan Yang)
>   6. Re: Histogram stretch (Karthik Krishnan)
>   7. Re: Software Guide (error report) (Luis Ibanez)
>   8. Order of libraries in Makefile (Einstein, Daniel R)
>   9. Re: Order of libraries in Makefile (Luis Ibanez)
>  10. Histogram equalization (Ken Urish)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 31 Aug 2005 11:11:10 -0500
> From: rvivanco at cs.umanitoba.ca
> Subject: [Insight-users] registration pipeline suggestion
> To: insight-users at itk.org
> Message-ID: <20050831111110.3o2irnczh8gwok4s at webmail.cs.umanitoba.ca>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
>
> The registration chapter of the user's guide is quite helpful and 
> extensive, but
> with the many options for registration I was wondering if someone could 
> give me
> a suggestion on which registration pipeline would work most of the times 
> for
> registering a functional dataset, by itself and also accross subjects.
>
> thanks,
> rodrigo
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 31 Aug 2005 12:12:06 -0400
> From: "Barbara Garita" <bgarita at ufl.edu>
> Subject: [Insight-users] Help creating a element in  ITK FEM
> To: <insight-users at itk.org>
> Message-ID: <001b01c5ae46$bbd9bd00$9933b29f at dbfvp>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I've been reading the code and trying to understand how to create an
> itkFEMElement of a bar (beam, truss) that is suited for 3D space.  The 
> line
> elements available are not suited for 3d space.  Where to start?  The
> documentation is distributed in every itkFEM file and difficult to follow
> for me.
>
> Thanks, Barbara.
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 31 Aug 2005 13:41:35 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] registration pipeline suggestion
> To: rvivanco at cs.umanitoba.ca
> Cc: insight-users at itk.org
> Message-ID: <4315EBCF.7080007 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Rodrigo,
>
>
> Is your functional dataset a fMRI image or a PET scan ?
>
>
> In general terms you may want to use a combination such as:
>
> A) METRIC
> Mutual Information metrics in ITK:
> http://www.itk.org/Insight/Doxygen/html/group__RegistrationMetrics.html
>
> B) TRANSFORM AND OPTIMIZER
> If you are registering a subject with itself you should
> use the Rigid Transform:
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1VersorRigid3DTransform.html
> and its associated optimizer
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1VersorRigid3DTransform.html
>
> If you are registering two different subjects you
> probably want the SimilarityTransform, or the AffineTransform.
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1Similarity3DTransform.html
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1AffineTransform.html
> Note that the Affine transform is more expensive to compute
> than the Similarity transform, and that functional datasets
> may not have the anatomical information that will justify
> deformations such as Shearing.
>
>
> C) INTERPOLATOR
> A linear interpolator is in general the best compromise
> between precision and performance.
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1LinearInterpolateImageFunction.html
> However if you are dealing with low resolution datasets you
> may affort a more time-expensive interpolator such as BSplines.
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1BSplineInterpolateImageFunction.html
>
>
> Also, you may want to give it a try to Slicer,
>
>             http://www.slicer.org/intro/
>
> Which already has a module for registration functional MRI based
> on ITK methods. Slicer is free and Open Source.
>
>
>
>    Regards,
>
>
>       Luis
>
>
>
> -------------------------------
> rvivanco at cs.umanitoba.ca wrote:
>> Hello,
>>
>> The registration chapter of the user's guide is quite helpful and 
>> extensive, but
>> with the many options for registration I was wondering if someone could 
>> give me
>> a suggestion on which registration pipeline would work most of the times 
>> for
>> registering a functional dataset, by itself and also accross subjects.
>>
>> thanks,
>> rodrigo
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 31 Aug 2005 10:42:41 -0400
> From: "Miller, James V (Research)" <millerjv at crd.ge.com>
> Subject: RE: [Insight-users] Local smoothing of a deformation field
> To: Val?rie Duay <valerie.duay at epfl.ch>, <insight-users at itk.org>
> Message-ID:
> <FA26BEF1EA775E4584FB34B91E14A1C403F35015 at SCHMLVEM01.e2k.ad.ge.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Valerie,
>
> Currently, you will have to write your own filter to take the
> deformation field as one input and the mask to operate on as another
> input. None of the smoothing filters currently support operating under
> a mask.
>
> You should be able to model this after the 
> itkNormalizedCorrelationImageFilter.
> This filter allows you to calculate of the normalized correlation of a 
> kernel
> across an image and restrict the calculation to just the pixels that are
> under the mask.
>
> We hope to contribute code that will allow any neighborhood operator
> to be applied under a mask but we have not had the time to prepare that
> code for inclusion in ITK.
>
> Jim
>
> -----Original Message-----
> From: insight-users-bounces+millerjv=crd.ge.com at itk.org
> [mailto:insight-users-bounces+millerjv=crd.ge.com at itk.org]On Behalf Of
> Valérie Duay
> Sent: Wednesday, August 31, 2005 9:55 AM
> To: insight-users at itk.org
> Subject: [Insight-users] Local smoothing of a deformation field
>
>
> Hello,
>
> I'd like to smooth a deformation field but locally. The areas to smooth
> are indicated on a binary image.
> What would be the best way to do that with the ITK library?
>
> Thanks,
>
> Valerie
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 31 Aug 2005 21:58:53 +0100
> From: Yan Yang <y.yang at apu.ac.uk>
> Subject: [Insight-users] Histogram stretch
> To: "insight-users at itk.org" <insight-users at itk.org>
> Message-ID: <1125521933.43161a0d0a4f8 at webmail.che.apu.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear All,
>
> I want to use Histogram stretch to increast image contrast. Could you tell
> me if there is Histogram Stretch function provided in ITK?
>
> Thanks in advance!
>
> Yan
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 31 Aug 2005 16:17:27 -0400
> From: Karthik Krishnan <Karthik.Krishnan at kitware.com>
> Subject: Re: [Insight-users] Histogram stretch
> To: y.yang at apu.ac.uk
> Cc: "insight-users at itk.org" <insight-users at itk.org>
> Message-ID: <43161057.60403 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1RescaleIntensityImageFilter.html
>
> are equivalent to linear streching of the intensity range.
>
> You may alternatively supply your own window level settings with
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1IntensityWindowingImageFilter.html
>
> If you are looking for histogram equalization methods to have your own
> presets, you can use
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1AdaptiveHistogramEqualizationImageFilter.html
>
> -karthik
>
>
>
> Yan Yang wrote:
>
>>Dear All,
>>
>>I want to use Histogram stretch to increast image contrast. Could you tell
>>me if there is Histogram Stretch function provided in ITK?
>>
>>Thanks in advance!
>>
>>Yan
>>_______________________________________________
>>Insight-users mailing list
>>Insight-users at itk.org
>>http://www.itk.org/mailman/listinfo/insight-users
>>
>>
>>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 31 Aug 2005 16:59:53 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] Software Guide (error report)
> To: wlzhu <wlzhu at nlpr.ia.ac.cn>
> Cc: Insight Users <insight-users at itk.org>
> Message-ID: <43161A49.6070504 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Winlin,
>
> Thanks for sending the details of the page where
> you found the error in the ITK Software Guide.
>
> You are right, the return type of SetPixel() must
> be "void" instead of "PixelType". We just committed
> a fix for this error in the CVS sources of the guide,
> and we will generate a corrected version of the PDF
> documents.
>
> Please let us know of any other error that you may
> find in the Software Guide.
>
>
>   Thanks a lot,
>
>
>      Luis
>
>
> -------------
> wlzhu wrote:
>> Hi, Luis,
>>       In the most updated version of  ITK Software Guide(25 July 2005), 
>> the error lies in paper number  709, where it writes
>> PixelType SetPixel(const unsigned int i, PixelType p).   Please check it.
>>
>>
>>
>> ----- Original Message ----- 
>> From: "Luis Ibanez" <luis.ibanez at kitware.com>
>> To: "wlzhu" <wlzhu at nlpr.ia.ac.cn>
>> Cc: <insight-users at itk.org>
>> Sent: Wednesday, August 31, 2005 12:46 AM
>> Subject: Re: [Insight-users] Software Guide (error report)
>>
>>
>>
>>>Hi Wanlin,
>>>
>>>Thanks for reporting the errors that you found in the
>>>ITK Software Guide.
>>>
>>>
>>>We are trying to locate the error that you mention but
>>>couldn't find it so far.
>>>
>>>Are you refering to page 719 as numbered in the PDF reader ?
>>>or as numbered in paper (the number on the top of the page) ?
>>>
>>>The ItkSoftwareGuide.2.0.0.pdf only has 663 pages...
>>>
>>>--
>>>
>>>The most updated version, that is available at:
>>>
>>>   http://www.itk.org/ItkSoftwareGuide.pdf
>>>
>>>has 819 pages, but none of the pages 719 (paper or pdf) has
>>>a SetPixel() in it.
>>>
>>>
>>>Our current guess is that you are refering to the instruction
>>>in PDF-page 744 (paper-page 712) which refers to how to setup
>>>the pixels in a Neighborhood iterator. In which case the statement
>>>is correct, because that method returns by reference a boolean
>>>representing the status result of the operation:
>>>
>>>http://www.itk.org/Insight/Doxygen/html/classitk_1_1NeighborhoodIterator.html#a7
>>>
>>>
>>>Could you please confirm if this is the case ?
>>>
>>>
>>>   Thanks
>>>
>>>
>>>     Luis
>>>
>>>
>>>
>>>---------------
>>>wlzhu wrote:
>>>
>>>>Hi, Schroeder,
>>>>
>>>>I find a mistake in ItkSoftwareGuide 2.0. Page 719. it should be
>>>>void SetPixel(const unsigned int i, pIxelType p);
>>>>
>>>>
>>>>best
>>>>
>>>>Wanlin
>>>>_______________________________________________
>>>>Insight-users mailing list
>>>>Insight-users at itk.org
>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>>
>>
>>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 31 Aug 2005 13:59:49 -0700
> From: "Einstein, Daniel R" <daniel.einstein at pnl.gov>
> Subject: [Insight-users] Order of libraries in Makefile
> To: insight-users at itk.org
> Message-ID:
> <0DF798CBF125BF4AA1227F26431C29BD01A33008 at pnlmse27.pnl.gov>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello,
>
> In trying to write images from my Qt application, I discovered - the
> hard way - that I had to move the reference to libitkgdm.a to
> immediately after libITKIO.a. CMAKE probably figures all of these things
> out. I am somewhat stuck using qmake. Any rules of thumb about the order
> in which the librbaries need to be listed in the Makefile?
>
> Dan
>
> Daniel R Einstein, PhD
> Biological Monitoring and Modeling
> Pacific Northwest National Laboratory
> P.O. Box 999; MSIN P7-59
> Richland, WA 99352
> Tel: 509/ 376-2924
> Fax: 509/376-9064
> daniel.einstein at pnl.gov
>
>
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> ------------------------------
>
> Message: 9
> Date: Wed, 31 Aug 2005 17:44:12 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] Order of libraries in Makefile
> To: "Einstein, Daniel R" <daniel.einstein at pnl.gov>
> Cc: insight-users at itk.org
> Message-ID: <431624AC.5040500 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Daniel,
>
> CMake does a nice job ordering the libraries according to
> their mutual dependencies.
>
> One easy thing you can do is to create a dummy CMake project
> using the same ITK libraries that you need for you QMake project,
> and then from the Makefile generated by CMake, take the order of
> libraries on the link rule line and copy it into your QMake project.
>
>
> Regards,
>
>
> Luis
>
>
>
> --------------------------
> Einstein, Daniel R wrote:
>> Hello,
>>
>> In trying to write images from my Qt application, I discovered - the
>> hard way - that I had to move the reference to libitkgdm.a to
>> immediately after libITKIO.a. CMAKE probably figures all of these things
>> out. I am somewhat stuck using qmake. Any rules of thumb about the order
>> in which the librbaries need to be listed in the Makefile?
>>
>> Dan
>>
>> Daniel R Einstein, PhD
>> Biological Monitoring and Modeling
>> Pacific Northwest National Laboratory
>> P.O. Box 999; MSIN P7-59
>> Richland, WA 99352
>> Tel: 509/ 376-2924
>> Fax: 509/376-9064
>> _daniel.einstein at pnl.gov_ <mailto:daniel.einstein at pnl.gov>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 31 Aug 2005 21:39:57 -0400
> From: Ken Urish <ken.urish at gmail.com>
> Subject: [Insight-users] Histogram equalization
> To: insight-users at itk.org
> Message-ID: <d9adedd805083118396f169ecf at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I saw on the itk list serve that lots of people have asked for a histogram
> equalization back in 2004. I didnt see it anywhere, but I cant believe it
> hasnt been done yet. Im just looking for a positive confirmation because I
> hate coding what has already been coded.
>
> Thanks
> --Ken--
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>
> End of Insight-users Digest, Vol 16, Issue 75
> *********************************************
>