[Insight-users] Q about header file of data download from Liver challenge 2007
Luis Ibanez
luis.ibanez at kitware.com
Mon May 28 17:23:07 EDT 2012
Hi Sergio,
Thanks for the clarification.
It is very unfortunate that the Challenges tend to
follow the practice of Closing Access to Data.
Such practice is contrary to the Ethical principles
of Scientific research and it is something that we,
as a Community has to work together to correct.
This is just Unacceptable.
Data should be Freely available to anyone, if we
are to exercise the Reproducibility Verification
practices that are at the root of true Scientific
work.
Data must be Open, and Re-Distributable.
Particularly if such data was gathered using
Public Funds.
The restrictive terms imposed in rules such as:
http://www.sliver07.org/rules.php
has not place in the future of Open Science.
This:
"Use of the data for any other purposes
requires explicit permission from the
maintainers of this site"
is simply absurd.
and so is this:
"Commercial use of segmentation algorithms
that use the supplied data (test or training
cases) as training material is forbidden."
Since,
most activities by University research groups
are indeed Commercial activities, despite their
common status of non-profit:
http://cyber.law.harvard.edu/people/tfisher/2002Madeyedit.html
All participants in this Challenge have already
violated the terms of use, simply because they
are legally inconsistent and poorly written.
This just show how few the Challenges have done
for promoting the progress of Science in our Field.
Simple competitive events that do not move the field
one inch forward. do not result in shared algorithms,
do not result in shared data. They only pursue the
amusement of ending with 1 Winner and (N-1)
Losers. The type of empty reputation that keeps
the medical image analysis field in its current
stagnation.
Luis
--------------------------------------------------
On Thu, May 24, 2012 at 3:36 AM, Sergio Vera <sergio.vera at alma3d.com> wrote:
> Luis,
> about your question regarding the public availability of the data:
>
> SLiver07 challenge data is free to download once you have registered your
> team and signed a document that states that you cannot share or show the
> data to anyone outside of your team. (http://www.sliver07.org/rules.php)
>
> This agreement has been used in some other MICCAI challenges as well.
>
> regards
>
> On Thu, May 24, 2012 at 3:13 AM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>
>>
>> Hi ekyaya,
>>
>>
>> Line 199 of itkImageBase.hxx
>>
>> says that your suspicions are well-founded:
>>
>> this->m_IndexToPhysicalPoint = this->m_Direction * scale;
>>
>> as well as lines 94-99 in the itkImageTransformHelper.h
>>
>> 94 inline static void TransformIndexToPhysicalPointCol(
>> 95 const MatrixType & matrix,
>> 96 const IndexType & index, DoublePoint & point,
>> 97 const UniqueTypeBoolFalse &)
>> 98 {
>> 99 point[R] = point[R] + matrix[R][C] * index[C];
>>
>>
>> The matrix in the MetaImage headers shouldn't have
>> combined the spacing with the direction cosines. This
>> composition is done for you in line 99 of the ImageBase
>> class.
>>
>> You may want to contact the organizers of the
>> challenge and ask for clarification.
>>
>>
>> BTW, Is this Challenge data available to the public ?
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> -------------------------
>>
>> On Mon, May 21, 2012 at 6:14 PM, erkang <ekyaya at gmail.com> wrote:
>>
>>> Hi everyone:
>>>
>>> I play with the meta data downloaded from Liver challenge 2007. However,
>>> I
>>> confused with the "TransformMatrix" item in the header file.
>>>
>>> One example of the header file is as following:
>>>
>>> ObjectType = Image
>>> NDims = 3
>>> BinaryData = True
>>> BinaryDataByteOrderMSB = False
>>> TransformMatrix = 0.74219 0 0 0 0.74219 0 0 0 1.5
>>> Offset = 0 0 0
>>> CenterOfRotation = 0 0 0
>>> ElementSpacing = 0.74219 0.74219 1.5
>>> DimSize = 512 512 183
>>> AnatomicalOrientation = ???
>>> ElementSize = 0.58594 0.58594 1
>>> ElementType = MET_SHORT
>>> ElementDataFile = liver-orig001.raw
>>>
>>> I doubt that the header files of these data are not correct. I check the
>>> metaIO in ITK. ITK does first read the direction (TransformMatrix ) and
>>> then
>>> multiplied by spacing. I test it in ImageFileReader and transform of the
>>> loaded image is 0.74219*0.74219 0 0 0 0.74219*0.74219 0 0 0 1.5*1.5.
>>>
>>> But, I would like to guess the "TransformMatrix" of the header file is
>>> TransformMatrix = 1 0 0 0 1 0 0 0 1. And after multiplied by spacing, the
>>> actual transform matrix is 0.74219 0 0 0 0.74219 0 0 0 1.5.
>>>
>>> Is that correct? Or what's the best way to load these data? Thanks.
>>>
>>> --
>>> View this message in context:
>>> http://itk-insight-users.2283740.n2.nabble.com/Q-about-header-file-of-data-download-from-Liver-challenge-2007-tp7570104.html
>>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
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>>
>>
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>
>
> --
> Sergio Vera
>
> Alma IT Systems
> C/ Vilana, 4B, 4º 1ª
> 08022 Barcelona
> T. (+34) 932 380 592
> www.alma3d.com
>
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