From nikelski at bic.mni.mcgill.ca  Tue May  1 10:39:31 2007
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Tue, 1 May 2007 10:39:31 -0400
Subject: [MINC-users] brain-view??
Message-ID: <e12172550705010739p69caafbdif86f1333643be1ef@mail.gmail.com>

Hi all,

   I am collaborating with a researcher who recollects using a piece of
BIC-developed software, called brain-view, sometime in the recent past.
Personally, I have never heard of it, and it isn't amongst the packages
distributed by BIC (I believe) ... although there is a link at
"http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
and Yorick seems to have some version of it running.

   Question: Is this software ready for use and being actively developed and
distributed (within the BIC community, at least)?  Or is this simply a
"proof of concept" project that isn''t going any further (as suggested in
the wiki). Are there better options?

Thanks,

-Jim


-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University

From anka at bic.mni.mcgill.ca  Tue May  1 14:48:14 2007
From: anka at bic.mni.mcgill.ca (Anka Kochanowska)
Date: Tue, 01 May 2007 14:48:14 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <e12172550705010739p69caafbdif86f1333643be1ef@mail.gmail.com>
References: <e12172550705010739p69caafbdif86f1333643be1ef@mail.gmail.com>
Message-ID: <46378B6E.9030705@bic.mni.mcgill.ca>

In Louis Collins' lab we have an IGNS project with few applications that 
allow you to view minc data or display obj files.
There is a simple program called MincView, based on vtk (5.0) with qt 
user interface.
As the project is not finished, there is no package ready for install, 
and I have not yet thought of creating it (I am the main developer on 
the project).

Anka


EJ Nikelski wrote:

>Hi all,
>
>   I am collaborating with a researcher who recollects using a piece of
>BIC-developed software, called brain-view, sometime in the recent past.
>Personally, I have never heard of it, and it isn't amongst the packages
>distributed by BIC (I believe) ... although there is a link at
>"http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
>and Yorick seems to have some version of it running.
>
>   Question: Is this software ready for use and being actively developed and
>distributed (within the BIC community, at least)?  Or is this simply a
>"proof of concept" project that isn''t going any further (as suggested in
>the wiki). Are there better options?
>
>Thanks,
>
>-Jim
>
>
>  
>

From nikelski at bic.mni.mcgill.ca  Tue May  1 19:12:48 2007
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Tue, 1 May 2007 19:12:48 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <46378B6E.9030705@bic.mni.mcgill.ca>
References: <e12172550705010739p69caafbdif86f1333643be1ef@mail.gmail.com>
	<46378B6E.9030705@bic.mni.mcgill.ca>
Message-ID: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>

Hi Anka,

   Are you looking for beta testers? We would be willing to test mincView,
particularly if it provides similar functionality to brain-view, i.e.
overlaying a cortical surface (obj) with functional or cortical thickness
data.  Just make the source and a make file available, and we can build it
ourselves.  We don't really need a package at this point ...

   BTW, do you know whether brain-view is really dead? It looks a bit dated
(QT3  with SoQT libraries and a very Inventor look to it).  If it is
officially dead, I shall recommend that we look for something else.

Thanks for the info,

-Jim



On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
>
> In Louis Collins' lab we have an IGNS project with few applications that
> allow you to view minc data or display obj files.
> There is a simple program called MincView, based on vtk (5.0) with qt
> user interface.
> As the project is not finished, there is no package ready for install,
> and I have not yet thought of creating it (I am the main developer on
> the project).
>
> Anka
>
>
> EJ Nikelski wrote:
>
> >Hi all,
> >
> >   I am collaborating with a researcher who recollects using a piece of
> >BIC-developed software, called brain-view, sometime in the recent past.
> >Personally, I have never heard of it, and it isn't amongst the packages
> >distributed by BIC (I believe) ... although there is a link at
> >"http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
> http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
> >and Yorick seems to have some version of it running.
> >
> >   Question: Is this software ready for use and being actively developed
> and
> >distributed (within the BIC community, at least)?  Or is this simply a
> >"proof of concept" project that isn''t going any further (as suggested in
> >the wiki). Are there better options?
> >
> >Thanks,
> >
> >-Jim
> >
> >
> >
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University
Tel: (514) 340-8222 x 2298
Fax: (514) 340-8295

From anka at bic.mni.mcgill.ca  Wed May  2 09:25:30 2007
From: anka at bic.mni.mcgill.ca (Anka Kochanowska)
Date: Wed, 02 May 2007 09:25:30 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
References: <e12172550705010739p69caafbdif86f1333643be1ef@mail.gmail.com>	<46378B6E.9030705@bic.mni.mcgill.ca>
	<e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
Message-ID: <4638914A.2040700@bic.mni.mcgill.ca>

Hi!
Beta testing  and source availability depends on my boss, prof. Louis 
Collins.
If the data is in the form .mnc or .obj, we can show it.
MincView is developed on Linux platform, but I have a Windows version 
just for the demo.

I don't know brain-view.

Thanks for the offer!

Anka



EJ Nikelski wrote:

>Hi Anka,
>
>   Are you looking for beta testers? We would be willing to test mincView,
>particularly if it provides similar functionality to brain-view, i.e.
>overlaying a cortical surface (obj) with functional or cortical thickness
>data.  Just make the source and a make file available, and we can build it
>ourselves.  We don't really need a package at this point ...
>
>   BTW, do you know whether brain-view is really dead? It looks a bit dated
>(QT3  with SoQT libraries and a very Inventor look to it).  If it is
>officially dead, I shall recommend that we look for something else.
>
>Thanks for the info,
>
>-Jim
>
>
>
>On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
>  
>
>>In Louis Collins' lab we have an IGNS project with few applications that
>>allow you to view minc data or display obj files.
>>There is a simple program called MincView, based on vtk (5.0) with qt
>>user interface.
>>As the project is not finished, there is no package ready for install,
>>and I have not yet thought of creating it (I am the main developer on
>>the project).
>>
>>Anka
>>
>>
>>EJ Nikelski wrote:
>>
>>    
>>
>>>Hi all,
>>>
>>>  I am collaborating with a researcher who recollects using a piece of
>>>BIC-developed software, called brain-view, sometime in the recent past.
>>>Personally, I have never heard of it, and it isn't amongst the packages
>>>distributed by BIC (I believe) ... although there is a link at
>>>"http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
>>>      
>>>
>>http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
>>    
>>
>>>and Yorick seems to have some version of it running.
>>>
>>>  Question: Is this software ready for use and being actively developed
>>>      
>>>
>>and
>>    
>>
>>>distributed (within the BIC community, at least)?  Or is this simply a
>>>"proof of concept" project that isn''t going any further (as suggested in
>>>the wiki). Are there better options?
>>>
>>>Thanks,
>>>
>>>-Jim
>>>
>>>
>>>
>>>
>>>      
>>>
>>_______________________________________________
>>MINC-users at bic.mni.mcgill.ca
>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>    
>>
>
>
>
>  
>

From jason at bic.mni.mcgill.ca  Wed May  2 09:38:21 2007
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 2 May 2007 09:38:21 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
References: <e12172550705010739p69caafbdif86f1333643be1ef@mail.gmail.com>
Message-ID: <4638944D.3080203@bic.mni.mcgill.ca>

EJ Nikelski wrote:
> Hi Anka,
>
>    Are you looking for beta testers? We would be willing to test mincView,
> particularly if it provides similar functionality to brain-view, i.e.
> overlaying a cortical surface (obj) with functional or cortical thickness
> data.  Just make the source and a make file available, and we can build it
> ourselves.  We don't really need a package at this point ...
>
>    BTW, do you know whether brain-view is really dead? It looks a bit dated
> (QT3  with SoQT libraries and a very Inventor look to it).  If it is
> officially dead, I shall recommend that we look for something else.
>   
Contrary to seemingly popular belief, brain-view is not dead (as an 
aside, why would having an Inventor look make it seem dead? I'll take 
Inventor or its derivatives over VTK any day). As far as I know you're 
welcome to it, unless anyone from Alan's group objects.

Jason
> Thanks for the info,
>
> -Jim
>
>
>
> On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
>   
>> In Louis Collins' lab we have an IGNS project with few applications that
>> allow you to view minc data or display obj files.
>> There is a simple program called MincView, based on vtk (5.0) with qt
>> user interface.
>> As the project is not finished, there is no package ready for install,
>> and I have not yet thought of creating it (I am the main developer on
>> the project).
>>
>> Anka
>>
>>
>> EJ Nikelski wrote:
>>
>>     
>>> Hi all,
>>>
>>>   I am collaborating with a researcher who recollects using a piece of
>>> BIC-developed software, called brain-view, sometime in the recent past.
>>> Personally, I have never heard of it, and it isn't amongst the packages
>>> distributed by BIC (I believe) ... although there is a link at
>>> "http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
>>>       
>> http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
>>     
>>> and Yorick seems to have some version of it running.
>>>
>>>   Question: Is this software ready for use and being actively developed
>>>       
>> and
>>     
>>> distributed (within the BIC community, at least)?  Or is this simply a
>>> "proof of concept" project that isn''t going any further (as suggested in
>>> the wiki). Are there better options?
>>>
>>> Thanks,
>>>
>>> -Jim
>>>
>>>
>>>
>>>
>>>       
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>     
>
>
>
>   


From nikelski at bic.mni.mcgill.ca  Wed May  2 10:07:23 2007
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Wed, 2 May 2007 10:07:23 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <4638944D.3080203@bic.mni.mcgill.ca>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
	<4638944D.3080203@bic.mni.mcgill.ca>
Message-ID: <e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>

Hi Jason,

   I shall defer to you on Inventor versus VTK issues. I assumed its death
due to its lack of presence and current documentation (not the look).
Assuming that no one from Alan's group objects, where might I find the most
current source and perhaps a make file? I would be perfectly willing to
cobble together a bit of documentation, if that would help.

-Jim


On 5/2/07, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
>
> EJ Nikelski wrote:
> > Hi Anka,
> >
> >    Are you looking for beta testers? We would be willing to test
> mincView,
> > particularly if it provides similar functionality to brain-view, i.e.
> > overlaying a cortical surface (obj) with functional or cortical
> thickness
> > data.  Just make the source and a make file available, and we can build
> it
> > ourselves.  We don't really need a package at this point ...
> >
> >    BTW, do you know whether brain-view is really dead? It looks a bit
> dated
> > (QT3  with SoQT libraries and a very Inventor look to it).  If it is
> > officially dead, I shall recommend that we look for something else.
> >
> Contrary to seemingly popular belief, brain-view is not dead (as an
> aside, why would having an Inventor look make it seem dead? I'll take
> Inventor or its derivatives over VTK any day). As far as I know you're
> welcome to it, unless anyone from Alan's group objects.
>
> Jason
> > Thanks for the info,
> >
> > -Jim
> >
> >
> >
> > On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
> >
> >> In Louis Collins' lab we have an IGNS project with few applications
> that
> >> allow you to view minc data or display obj files.
> >> There is a simple program called MincView, based on vtk (5.0) with qt
> >> user interface.
> >> As the project is not finished, there is no package ready for install,
> >> and I have not yet thought of creating it (I am the main developer on
> >> the project).
> >>
> >> Anka
> >>
> >>
> >> EJ Nikelski wrote:
> >>
> >>
> >>> Hi all,
> >>>
> >>>   I am collaborating with a researcher who recollects using a piece of
> >>> BIC-developed software, called brain-view, sometime in the recent
> past.
> >>> Personally, I have never heard of it, and it isn't amongst the
> packages
> >>> distributed by BIC (I believe) ... although there is a link at
> >>> "http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
> >>>
> >> http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
> >>
> >>> and Yorick seems to have some version of it running.
> >>>
> >>>   Question: Is this software ready for use and being actively
> developed
> >>>
> >> and
> >>
> >>> distributed (within the BIC community, at least)?  Or is this simply a
> >>> "proof of concept" project that isn''t going any further (as suggested
> in
> >>> the wiki). Are there better options?
> >>>
> >>> Thanks,
> >>>
> >>> -Jim
> >>>
> >>>
> >>>
> >>>
> >>>
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >>
> >
> >
> >
> >
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University
Tel: (514) 340-8222 x 2298
Fax: (514) 340-8295

From a.janke at gmail.com  Wed May  2 10:10:47 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 3 May 2007 00:10:47 +1000
Subject: [MINC-users] brain-view??
In-Reply-To: <e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
	<4638944D.3080203@bic.mni.mcgill.ca>
	<e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>
Message-ID: <d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>

Hi Jim,

I am in the throes of compiling a Ubuntu/Debian package for brain-view
for you.  As for documentation I would suggest that put it together on
wiki.bic.mni.mcgill.ca


a

On 5/3/07, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
> Hi Jason,
>
>    I shall defer to you on Inventor versus VTK issues. I assumed its death
> due to its lack of presence and current documentation (not the look).
> Assuming that no one from Alan's group objects, where might I find the most
> current source and perhaps a make file? I would be perfectly willing to
> cobble together a bit of documentation, if that would help.
>
> -Jim
>
>
> On 5/2/07, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> >
> > EJ Nikelski wrote:
> > > Hi Anka,
> > >
> > >    Are you looking for beta testers? We would be willing to test
> > mincView,
> > > particularly if it provides similar functionality to brain-view, i.e.
> > > overlaying a cortical surface (obj) with functional or cortical
> > thickness
> > > data.  Just make the source and a make file available, and we can build
> > it
> > > ourselves.  We don't really need a package at this point ...
> > >
> > >    BTW, do you know whether brain-view is really dead? It looks a bit
> > dated
> > > (QT3  with SoQT libraries and a very Inventor look to it).  If it is
> > > officially dead, I shall recommend that we look for something else.
> > >
> > Contrary to seemingly popular belief, brain-view is not dead (as an
> > aside, why would having an Inventor look make it seem dead? I'll take
> > Inventor or its derivatives over VTK any day). As far as I know you're
> > welcome to it, unless anyone from Alan's group objects.
> >
> > Jason
> > > Thanks for the info,
> > >
> > > -Jim
> > >
> > >
> > >
> > > On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
> > >
> > >> In Louis Collins' lab we have an IGNS project with few applications
> > that
> > >> allow you to view minc data or display obj files.
> > >> There is a simple program called MincView, based on vtk (5.0) with qt
> > >> user interface.
> > >> As the project is not finished, there is no package ready for install,
> > >> and I have not yet thought of creating it (I am the main developer on
> > >> the project).
> > >>
> > >> Anka
> > >>
> > >>
> > >> EJ Nikelski wrote:
> > >>
> > >>
> > >>> Hi all,
> > >>>
> > >>>   I am collaborating with a researcher who recollects using a piece of
> > >>> BIC-developed software, called brain-view, sometime in the recent
> > past.
> > >>> Personally, I have never heard of it, and it isn't amongst the
> > packages
> > >>> distributed by BIC (I believe) ... although there is a link at
> > >>> "http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
> > >>>
> > >> http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
> > >>
> > >>> and Yorick seems to have some version of it running.
> > >>>
> > >>>   Question: Is this software ready for use and being actively
> > developed
> > >>>
> > >> and
> > >>
> > >>> distributed (within the BIC community, at least)?  Or is this simply a
> > >>> "proof of concept" project that isn''t going any further (as suggested
> > in
> > >>> the wiki). Are there better options?
> > >>>
> > >>> Thanks,
> > >>>
> > >>> -Jim
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >> _______________________________________________
> > >> MINC-users at bic.mni.mcgill.ca
> > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >>
> > >>
> > >
> > >
> > >
> > >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
>
> --
> =================================
> Jim Nikelski, Ph.D.
> Postdoctoral Research Fellow
> Bloomfield Centre for Research in Aging
> Lady Davis Institute for Medical Research
> Sir Mortimer B. Davis - Jewish General Hospital
> McGill University
> Tel: (514) 340-8222 x 2298
> Fax: (514) 340-8295
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From jason at bic.mni.mcgill.ca  Wed May  2 10:10:33 2007
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 2 May 2007 10:10:33 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
Message-ID: <46389BD9.9070701@bic.mni.mcgill.ca>

Greetings again,

Andrew is working on a .deb package (and might have source tarballs as 
well - Andrew?), and there are application bundles for OS X kicking 
around too. If neither of that suits you I can give you the sources as 
tarballs.

Jason

EJ Nikelski wrote:
> Hi Jason,
>
>    I shall defer to you on Inventor versus VTK issues. I assumed its death
> due to its lack of presence and current documentation (not the look).
> Assuming that no one from Alan's group objects, where might I find the most
> current source and perhaps a make file? I would be perfectly willing to
> cobble together a bit of documentation, if that would help.
>
> -Jim
>
>
> On 5/2/07, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
>   
>> EJ Nikelski wrote:
>>     
>>> Hi Anka,
>>>
>>>    Are you looking for beta testers? We would be willing to test
>>>       
>> mincView,
>>     
>>> particularly if it provides similar functionality to brain-view, i.e.
>>> overlaying a cortical surface (obj) with functional or cortical
>>>       
>> thickness
>>     
>>> data.  Just make the source and a make file available, and we can build
>>>       
>> it
>>     
>>> ourselves.  We don't really need a package at this point ...
>>>
>>>    BTW, do you know whether brain-view is really dead? It looks a bit
>>>       
>> dated
>>     
>>> (QT3  with SoQT libraries and a very Inventor look to it).  If it is
>>> officially dead, I shall recommend that we look for something else.
>>>
>>>       
>> Contrary to seemingly popular belief, brain-view is not dead (as an
>> aside, why would having an Inventor look make it seem dead? I'll take
>> Inventor or its derivatives over VTK any day). As far as I know you're
>> welcome to it, unless anyone from Alan's group objects.
>>
>> Jason
>>     
>>> Thanks for the info,
>>>
>>> -Jim
>>>
>>>
>>>
>>> On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
>>>
>>>       
>>>> In Louis Collins' lab we have an IGNS project with few applications
>>>>         
>> that
>>     
>>>> allow you to view minc data or display obj files.
>>>> There is a simple program called MincView, based on vtk (5.0) with qt
>>>> user interface.
>>>> As the project is not finished, there is no package ready for install,
>>>> and I have not yet thought of creating it (I am the main developer on
>>>> the project).
>>>>
>>>> Anka
>>>>
>>>>
>>>> EJ Nikelski wrote:
>>>>
>>>>
>>>>         
>>>>> Hi all,
>>>>>
>>>>>   I am collaborating with a researcher who recollects using a piece of
>>>>> BIC-developed software, called brain-view, sometime in the recent
>>>>>           
>> past.
>>     
>>>>> Personally, I have never heard of it, and it isn't amongst the
>>>>>           
>> packages
>>     
>>>>> distributed by BIC (I believe) ... although there is a link at
>>>>> "http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
>>>>>
>>>>>           
>>>> http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
>>>>
>>>>         
>>>>> and Yorick seems to have some version of it running.
>>>>>
>>>>>   Question: Is this software ready for use and being actively
>>>>>           
>> developed
>>     
>>>> and
>>>>
>>>>         
>>>>> distributed (within the BIC community, at least)?  Or is this simply a
>>>>> "proof of concept" project that isn''t going any further (as suggested
>>>>>           
>> in
>>     
>>>>> the wiki). Are there better options?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> -Jim
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>           
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>>>
>>>>         
>>>
>>>
>>>       
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>     
>
>
>
>   


From sylvain at bic.mni.mcgill.ca  Wed May  2 10:17:25 2007
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Wed, 2 May 2007 10:17:25 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
	<4638944D.3080203@bic.mni.mcgill.ca>
	<e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>
	<d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>
Message-ID: <Pine.SGI.4.58.0705021014530.11460784@yorick.bic.mni.mcgill.ca>


I do have a debian package already, albeit it requires a small update. But
by the time you read this, Andrew will have finished I guess :-)

S

On Thu, 3 May 2007, Andrew Janke wrote:

> Hi Jim,
>
> I am in the throes of compiling a Ubuntu/Debian package for brain-view
> for you.  As for documentation I would suggest that put it together on
> wiki.bic.mni.mcgill.ca
>
>
> a
>
> On 5/3/07, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
> > Hi Jason,
> >
> >    I shall defer to you on Inventor versus VTK issues. I assumed its death
> > due to its lack of presence and current documentation (not the look).
> > Assuming that no one from Alan's group objects, where might I find the most
> > current source and perhaps a make file? I would be perfectly willing to
> > cobble together a bit of documentation, if that would help.
> >
> > -Jim
> >
> >
> > On 5/2/07, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> > >
> > > EJ Nikelski wrote:
> > > > Hi Anka,
> > > >
> > > >    Are you looking for beta testers? We would be willing to test
> > > mincView,
> > > > particularly if it provides similar functionality to brain-view, i.e.
> > > > overlaying a cortical surface (obj) with functional or cortical
> > > thickness
> > > > data.  Just make the source and a make file available, and we can build
> > > it
> > > > ourselves.  We don't really need a package at this point ...
> > > >
> > > >    BTW, do you know whether brain-view is really dead? It looks a bit
> > > dated
> > > > (QT3  with SoQT libraries and a very Inventor look to it).  If it is
> > > > officially dead, I shall recommend that we look for something else.
> > > >
> > > Contrary to seemingly popular belief, brain-view is not dead (as an
> > > aside, why would having an Inventor look make it seem dead? I'll take
> > > Inventor or its derivatives over VTK any day). As far as I know you're
> > > welcome to it, unless anyone from Alan's group objects.
> > >
> > > Jason
> > > > Thanks for the info,
> > > >
> > > > -Jim
> > > >
> > > >
> > > >
> > > > On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
> > > >
> > > >> In Louis Collins' lab we have an IGNS project with few applications
> > > that
> > > >> allow you to view minc data or display obj files.
> > > >> There is a simple program called MincView, based on vtk (5.0) with qt
> > > >> user interface.
> > > >> As the project is not finished, there is no package ready for install,
> > > >> and I have not yet thought of creating it (I am the main developer on
> > > >> the project).
> > > >>
> > > >> Anka
> > > >>
> > > >>
> > > >> EJ Nikelski wrote:
> > > >>
> > > >>
> > > >>> Hi all,
> > > >>>
> > > >>>   I am collaborating with a researcher who recollects using a piece of
> > > >>> BIC-developed software, called brain-view, sometime in the recent
> > > past.
> > > >>> Personally, I have never heard of it, and it isn't amongst the
> > > packages
> > > >>> distributed by BIC (I believe) ... although there is a link at
> > > >>> "http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
> > > >>>
> > > >> http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
> > > >>
> > > >>> and Yorick seems to have some version of it running.
> > > >>>
> > > >>>   Question: Is this software ready for use and being actively
> > > developed
> > > >>>
> > > >> and
> > > >>
> > > >>> distributed (within the BIC community, at least)?  Or is this simply a
> > > >>> "proof of concept" project that isn''t going any further (as suggested
> > > in
> > > >>> the wiki). Are there better options?
> > > >>>
> > > >>> Thanks,
> > > >>>
> > > >>> -Jim
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >> _______________________________________________
> > > >> MINC-users at bic.mni.mcgill.ca
> > > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >>
> > > >>
> > > >
> > > >
> > > >
> > > >
> > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> >
> >
> > --
> > =================================
> > Jim Nikelski, Ph.D.
> > Postdoctoral Research Fellow
> > Bloomfield Centre for Research in Aging
> > Lady Davis Institute for Medical Research
> > Sir Mortimer B. Davis - Jewish General Hospital
> > McGill University
> > Tel: (514) 340-8222 x 2298
> > Fax: (514) 340-8295
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (bicadmin at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4

From a.janke at gmail.com  Wed May  2 14:01:52 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 3 May 2007 04:01:52 +1000
Subject: [MINC-users] brain-view??
In-Reply-To: <d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>
	<4638944D.3080203@bic.mni.mcgill.ca>
	<e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>
	<d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>
Message-ID: <d747ed50705021101o2727d2a6q80e73cbc121d41b1@mail.gmail.com>

Well after a couple of hours work, I am well on the way...  The major
hurdle has been that there are 4 other BIC specific libraries that
brain-view depends upon, none of these have been released before
either (that I know of) and thus all required a fair amount of tidying
up so that I could make a source release as well as binary.

I am now finally up to brain-view so I should be abe to have a package
to you sometime tomorrow around this time..

stay tuned.


a

On 5/3/07, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Jim,
>
> I am in the throes of compiling a Ubuntu/Debian package for brain-view
> for you.  As for documentation I would suggest that put it together on
> wiki.bic.mni.mcgill.ca
>
>
> a
>
> On 5/3/07, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
> > Hi Jason,
> >
> >    I shall defer to you on Inventor versus VTK issues. I assumed its death
> > due to its lack of presence and current documentation (not the look).
> > Assuming that no one from Alan's group objects, where might I find the most
> > current source and perhaps a make file? I would be perfectly willing to
> > cobble together a bit of documentation, if that would help.
> >
> > -Jim
> >
> >
> > On 5/2/07, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> > >
> > > EJ Nikelski wrote:
> > > > Hi Anka,
> > > >
> > > >    Are you looking for beta testers? We would be willing to test
> > > mincView,
> > > > particularly if it provides similar functionality to brain-view, i.e.
> > > > overlaying a cortical surface (obj) with functional or cortical
> > > thickness
> > > > data.  Just make the source and a make file available, and we can build
> > > it
> > > > ourselves.  We don't really need a package at this point ...
> > > >
> > > >    BTW, do you know whether brain-view is really dead? It looks a bit
> > > dated
> > > > (QT3  with SoQT libraries and a very Inventor look to it).  If it is
> > > > officially dead, I shall recommend that we look for something else.
> > > >
> > > Contrary to seemingly popular belief, brain-view is not dead (as an
> > > aside, why would having an Inventor look make it seem dead? I'll take
> > > Inventor or its derivatives over VTK any day). As far as I know you're
> > > welcome to it, unless anyone from Alan's group objects.
> > >
> > > Jason
> > > > Thanks for the info,
> > > >
> > > > -Jim
> > > >
> > > >
> > > >
> > > > On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
> > > >
> > > >> In Louis Collins' lab we have an IGNS project with few applications
> > > that
> > > >> allow you to view minc data or display obj files.
> > > >> There is a simple program called MincView, based on vtk (5.0) with qt
> > > >> user interface.
> > > >> As the project is not finished, there is no package ready for install,
> > > >> and I have not yet thought of creating it (I am the main developer on
> > > >> the project).
> > > >>
> > > >> Anka
> > > >>
> > > >>
> > > >> EJ Nikelski wrote:
> > > >>
> > > >>
> > > >>> Hi all,
> > > >>>
> > > >>>   I am collaborating with a researcher who recollects using a piece of
> > > >>> BIC-developed software, called brain-view, sometime in the recent
> > > past.
> > > >>> Personally, I have never heard of it, and it isn't amongst the
> > > packages
> > > >>> distributed by BIC (I believe) ... although there is a link at
> > > >>> "http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
> > > >>>
> > > >> http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
> > > >>
> > > >>> and Yorick seems to have some version of it running.
> > > >>>
> > > >>>   Question: Is this software ready for use and being actively
> > > developed
> > > >>>
> > > >> and
> > > >>
> > > >>> distributed (within the BIC community, at least)?  Or is this simply a
> > > >>> "proof of concept" project that isn''t going any further (as suggested
> > > in
> > > >>> the wiki). Are there better options?
> > > >>>
> > > >>> Thanks,
> > > >>>
> > > >>> -Jim
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >> _______________________________________________
> > > >> MINC-users at bic.mni.mcgill.ca
> > > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >>
> > > >>
> > > >
> > > >
> > > >
> > > >
> > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> >
> >
> > --
> > =================================
> > Jim Nikelski, Ph.D.
> > Postdoctoral Research Fellow
> > Bloomfield Centre for Research in Aging
> > Lady Davis Institute for Medical Research
> > Sir Mortimer B. Davis - Jewish General Hospital
> > McGill University
> > Tel: (514) 340-8222 x 2298
> > Fax: (514) 340-8295
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From anka at bic.mni.mcgill.ca  Wed May  2 15:33:46 2007
From: anka at bic.mni.mcgill.ca (Anka Kochanowska)
Date: Wed, 02 May 2007 15:33:46 -0400
Subject: [MINC-users] brain-view??
In-Reply-To: <d747ed50705021101o2727d2a6q80e73cbc121d41b1@mail.gmail.com>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>	<4638944D.3080203@bic.mni.mcgill.ca>	<e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>	<d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>
	<d747ed50705021101o2727d2a6q80e73cbc121d41b1@mail.gmail.com>
Message-ID: <4638E79A.2020404@bic.mni.mcgill.ca>

Hi!
Will it be available on the web?
If not, could I also get a copy, please?
Must be about 3 am at your place, have a nice morning!
Anka


Andrew Janke wrote:

>Well after a couple of hours work, I am well on the way...  The major
>hurdle has been that there are 4 other BIC specific libraries that
>brain-view depends upon, none of these have been released before
>either (that I know of) and thus all required a fair amount of tidying
>up so that I could make a source release as well as binary.
>
>I am now finally up to brain-view so I should be abe to have a package
>to you sometime tomorrow around this time..
>
>stay tuned.
>
>
>a
>
>On 5/3/07, Andrew Janke <a.janke at gmail.com> wrote:
>  
>
>>Hi Jim,
>>
>>I am in the throes of compiling a Ubuntu/Debian package for brain-view
>>for you.  As for documentation I would suggest that put it together on
>>wiki.bic.mni.mcgill.ca
>>
>>
>>a
>>
>>On 5/3/07, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
>>    
>>
>>>Hi Jason,
>>>
>>>   I shall defer to you on Inventor versus VTK issues. I assumed its death
>>>due to its lack of presence and current documentation (not the look).
>>>Assuming that no one from Alan's group objects, where might I find the most
>>>current source and perhaps a make file? I would be perfectly willing to
>>>cobble together a bit of documentation, if that would help.
>>>
>>>-Jim
>>>
>>>
>>>On 5/2/07, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
>>>      
>>>
>>>>EJ Nikelski wrote:
>>>>        
>>>>
>>>>>Hi Anka,
>>>>>
>>>>>   Are you looking for beta testers? We would be willing to test
>>>>>          
>>>>>
>>>>mincView,
>>>>        
>>>>
>>>>>particularly if it provides similar functionality to brain-view, i.e.
>>>>>overlaying a cortical surface (obj) with functional or cortical
>>>>>          
>>>>>
>>>>thickness
>>>>        
>>>>
>>>>>data.  Just make the source and a make file available, and we can build
>>>>>          
>>>>>
>>>>it
>>>>        
>>>>
>>>>>ourselves.  We don't really need a package at this point ...
>>>>>
>>>>>   BTW, do you know whether brain-view is really dead? It looks a bit
>>>>>          
>>>>>
>>>>dated
>>>>        
>>>>
>>>>>(QT3  with SoQT libraries and a very Inventor look to it).  If it is
>>>>>officially dead, I shall recommend that we look for something else.
>>>>>
>>>>>          
>>>>>
>>>>Contrary to seemingly popular belief, brain-view is not dead (as an
>>>>aside, why would having an Inventor look make it seem dead? I'll take
>>>>Inventor or its derivatives over VTK any day). As far as I know you're
>>>>welcome to it, unless anyone from Alan's group objects.
>>>>
>>>>Jason
>>>>        
>>>>
>>>>>Thanks for the info,
>>>>>
>>>>>-Jim
>>>>>
>>>>>
>>>>>
>>>>>On 5/1/07, Anka Kochanowska <anka at bic.mni.mcgill.ca> wrote:
>>>>>
>>>>>          
>>>>>
>>>>>>In Louis Collins' lab we have an IGNS project with few applications
>>>>>>            
>>>>>>
>>>>that
>>>>        
>>>>
>>>>>>allow you to view minc data or display obj files.
>>>>>>There is a simple program called MincView, based on vtk (5.0) with qt
>>>>>>user interface.
>>>>>>As the project is not finished, there is no package ready for install,
>>>>>>and I have not yet thought of creating it (I am the main developer on
>>>>>>the project).
>>>>>>
>>>>>>Anka
>>>>>>
>>>>>>
>>>>>>EJ Nikelski wrote:
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>Hi all,
>>>>>>>
>>>>>>>  I am collaborating with a researcher who recollects using a piece of
>>>>>>>BIC-developed software, called brain-view, sometime in the recent
>>>>>>>              
>>>>>>>
>>>>past.
>>>>        
>>>>
>>>>>>>Personally, I have never heard of it, and it isn't amongst the
>>>>>>>              
>>>>>>>
>>>>packages
>>>>        
>>>>
>>>>>>>distributed by BIC (I believe) ... although there is a link at
>>>>>>>"http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev"<
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>http://wiki.bic.mni.mcgill.ca/index.php/BrainViewDev>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>and Yorick seems to have some version of it running.
>>>>>>>
>>>>>>>  Question: Is this software ready for use and being actively
>>>>>>>              
>>>>>>>
>>>>developed
>>>>        
>>>>
>>>>>>and
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>distributed (within the BIC community, at least)?  Or is this simply a
>>>>>>>"proof of concept" project that isn''t going any further (as suggested
>>>>>>>              
>>>>>>>
>>>>in
>>>>        
>>>>
>>>>>>>the wiki). Are there better options?
>>>>>>>
>>>>>>>Thanks,
>>>>>>>
>>>>>>>-Jim
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>_______________________________________________
>>>>>>MINC-users at bic.mni.mcgill.ca
>>>>>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>_______________________________________________
>>>>MINC-users at bic.mni.mcgill.ca
>>>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>>
>>>>        
>>>>
>>>
>>>--
>>>=================================
>>>Jim Nikelski, Ph.D.
>>>Postdoctoral Research Fellow
>>>Bloomfield Centre for Research in Aging
>>>Lady Davis Institute for Medical Research
>>>Sir Mortimer B. Davis - Jewish General Hospital
>>>McGill University
>>>Tel: (514) 340-8222 x 2298
>>>Fax: (514) 340-8295
>>>_______________________________________________
>>>MINC-users at bic.mni.mcgill.ca
>>>http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>>      
>>>
>>--
>>Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
>>Canberra->Australia    +61 (402) 700 883
>>
>>    
>>
>
>
>  
>

From anka at bic.mni.mcgill.ca  Thu May  3 09:24:05 2007
From: anka at bic.mni.mcgill.ca (Anka Kochanowska)
Date: Thu, 03 May 2007 09:24:05 -0400
Subject: [MINC-users] MincView
In-Reply-To: <4638E79A.2020404@bic.mni.mcgill.ca>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>	<4638944D.3080203@bic.mni.mcgill.ca>	<e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>	<d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>	<d747ed50705021101o2727d2a6q80e73cbc121d41b1@mail.gmail.com>
	<4638E79A.2020404@bic.mni.mcgill.ca>
Message-ID: <4639E275.1080309@bic.mni.mcgill.ca>

Hi!
I have prof. Louis Collins' OK to prepare MincView for beta testing and 
give it to anyone who wants it.
Please, bear with me, it will take a moment to extract MincView from a 
larger project.

MincView works with Qt 3.3 and VTK 5.0 (based on OpenGL) with CMake 2.4 
patch 3. I tried newer Cmake and it did not work. MincView is developed 
on Linux platform.
I will make a source tarball and you will have to build it.

MincView may be used to view .mnc files and .obj files.

Anka





From abraham.gedamu at gmail.com  Sun May  6 10:49:30 2007
From: abraham.gedamu at gmail.com (Abraham Gedamu)
Date: Sun, 6 May 2007 10:49:30 -0400
Subject: [MINC-users] minccalc
Message-ID: <a4f06d1e0705060749v42ec10a3wad14386573f312f6@mail.gmail.com>

Hi,

I want to do something simple with minccalc.  I have an input image (in.mnc)
and a mask (mask.mnc).  I want to set every voxel in the masked region of
the input image to a value, X.  Every voxel that is not within the masked
region gets assigned a value of Y*original voxel intensity.  I did the
following:

minccalc -expression "A[1] >= 1 ? 100 : A[0]*5" in.mnc mask.mnc out.mnc

When I look at out.mnc, the voxel intensities in the image do not represent
the values they should.

Any ideas?

Thanks,

Abe

From a.janke at gmail.com  Sun May  6 11:02:51 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 7 May 2007 01:02:51 +1000
Subject: [MINC-users] minccalc
In-Reply-To: <a4f06d1e0705060749v42ec10a3wad14386573f312f6@mail.gmail.com>
References: <a4f06d1e0705060749v42ec10a3wad14386573f312f6@mail.gmail.com>
Message-ID: <d747ed50705060802p1d97cbfbpecff2b8dfd5dfeaa@mail.gmail.com>

Looks right to me,

Sure you aren't getting bitten by a datatype and range issue?  What
type is your input image? byte?  by default minccalc will use the
datatype of the first input image for the output.

Perhaps add a -double in there and see if you then get what you are
expecting.  Beyond this you are going to have to provide a bit more
info than "not what they should be"... :)


a


On 5/7/07, Abraham Gedamu <abraham.gedamu at gmail.com> wrote:
> Hi,
>
> I want to do something simple with minccalc.  I have an input image (in.mnc)
> and a mask (mask.mnc).  I want to set every voxel in the masked region of
> the input image to a value, X.  Every voxel that is not within the masked
> region gets assigned a value of Y*original voxel intensity.  I did the
> following:
>
> minccalc -expression "A[1] >= 1 ? 100 : A[0]*5" in.mnc mask.mnc out.mnc
>
> When I look at out.mnc, the voxel intensities in the image do not represent
> the values they should.
>
> Any ideas?
>
> Thanks,
>
> Abe
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From abraham.gedamu at gmail.com  Sun May  6 15:04:27 2007
From: abraham.gedamu at gmail.com (Abraham Gedamu)
Date: Sun, 6 May 2007 15:04:27 -0400
Subject: [MINC-users] minccalc
In-Reply-To: <a4f06d1e0705060749v42ec10a3wad14386573f312f6@mail.gmail.com>
References: <a4f06d1e0705060749v42ec10a3wad14386573f312f6@mail.gmail.com>
Message-ID: <a4f06d1e0705061204x30d0f8c4ldd5c6cc4090e93af@mail.gmail.com>

Hey Andrew,

It was a datatype/range issue.

Thanks,

Abe

On 5/6/07, Abraham Gedamu <abraham.gedamu at gmail.com> wrote:
>
> Hi,
>
> I want to do something simple with minccalc.  I have an input image (
> in.mnc) and a mask (mask.mnc).  I want to set every voxel in the masked
> region of the input image to a value, X.  Every voxel that is not within the
> masked region gets assigned a value of Y*original voxel intensity.  I did
> the following:
>
> minccalc -expression "A[1] >= 1 ? 100 : A[0]*5" in.mnc mask.mnc out.mnc
>
> When I look at out.mnc, the voxel intensities in the image do not
> represent the values they should.
>
> Any ideas?
>
> Thanks,
>
> Abe
>

From acveilleux at mrs.mni.mcgill.ca  Sun May  6 23:02:34 2007
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Sun, 6 May 2007 23:02:34 -0400
Subject: [MINC-users] minccalc
In-Reply-To: <a4f06d1e0705060749v42ec10a3wad14386573f312f6@mail.gmail.com>;
	from abraham.gedamu@gmail.com on Sun, May 06, 2007 at 10:49:30AM
	-0400
References: <a4f06d1e0705060749v42ec10a3wad14386573f312f6@mail.gmail.com>
Message-ID: <20070506230234.A7076@mrs.mni.mcgill.ca>


	There must be a better way, but what about:

(1) Extract the masked voxels into a new minc files where every non-masked
    voxel is zero. (I.e.: mincmath -mult). Binarize it (mincmath -seg) and
    then multiply it with X. I'm too lazy to check if -seg makes the first
    step redundant.

(2) Extract the non-masked voxels into a new minc files where every masked
    voxel is zero (I.e.: mincmath -mult) and then multiply all voxels by Y.

(3) mincmath -add the output of (1) and (2) above.

Alex

On Sun, May 06, 2007 at 10:49:30AM -0400, Abraham Gedamu wrote:
> Date: Sun, 6 May 2007 10:49:30 -0400
> From: "Abraham Gedamu" <abraham.gedamu at gmail.com>
> To: minc-users at bic.mni.mcgill.ca
> Subject: [MINC-users] minccalc
> 
> Hi,
> 
> I want to do something simple with minccalc.  I have an input image (in.mnc)
> and a mask (mask.mnc).  I want to set every voxel in the masked region of
> the input image to a value, X.  Every voxel that is not within the masked
> region gets assigned a value of Y*original voxel intensity.  I did the
> following:
> 
> minccalc -expression "A[1] >= 1 ? 100 : A[0]*5" in.mnc mask.mnc out.mnc
> 
> When I look at out.mnc, the voxel intensities in the image do not represent
> the values they should.
> 
> Any ideas?
> 
> Thanks,
> 
> Abe
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From anka at bic.mni.mcgill.ca  Mon May  7 10:07:30 2007
From: anka at bic.mni.mcgill.ca (Anka Kochanowska)
Date: Mon, 07 May 2007 10:07:30 -0400
Subject: [MINC-users] MincView
In-Reply-To: <4639E275.1080309@bic.mni.mcgill.ca>
References: <e12172550705011612i3c4197c3kbb95d760ebed7aca@mail.gmail.com>	<4638944D.3080203@bic.mni.mcgill.ca>	<e12172550705020707l2567bbb6ldeae8d2fdb4b50b9@mail.gmail.com>	<d747ed50705020710x6058fa5bged4f50dad90a62cb@mail.gmail.com>	<d747ed50705021101o2727d2a6q80e73cbc121d41b1@mail.gmail.com>	<4638E79A.2020404@bic.mni.mcgill.ca>
	<4639E275.1080309@bic.mni.mcgill.ca>
Message-ID: <463F32A2.20507@bic.mni.mcgill.ca>

Hi!
I put mincview-1.0.1B.tar.gz in http://packages.bic.mni.mcgill.ca/tgz/
Please email me if you have questions.
Thanks for your interest!
Anka


From a.janke at gmail.com  Thu May 10 12:01:44 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 11 May 2007 02:01:44 +1000
Subject: [MINC-users] brain-view binary (and source packages).
Message-ID: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>

Finally I have this done,

get it fresh from:

   packages.bic.mni.mcgil.ca/deb

or in source from

   packages.bic.mni.mcgill.ca/tgz

Note that this thing has a heap of dependencies that I have no
included as pre-requisites in the package if only because I am sure
there are a few versions of COIN and the likes out there.

So, on my system (ubuntu feisty), I had to install these packages.

   apt-get install libpcre3 libglut3 libxmu6 libxi6 libcoin40c2
libqt3-mt libsoqt20

once you have these and the packages line in your sources.list just type:

   apt-get install brain-view




------


Now if you want to build it from source (hey there are those out there
who might like to).

you will need to download these source packages from /tgz

   arguments-0.2.1.tar.gz
   bicInventor-0.3.1.tar.gz
   oobicpl-0.4.3.tar.gz
   brain-view-0.6.2.tar.gz

and them make them in that order.  Of course you will also (if you are
on a debian system have to install this lot:

   apt-get install libpcre3-dev libglut3-dev libxmu-dev libxi-dev \
      libcoin40-dev libqt3-mt-dev libsoqt-dev

and you still wont be finished as then you will have to (if you are on
ubuntu) go and get these:

   libpcre++-dev_0.9.5-2_i386.deb
   libpcre++0_0.9.5-2_i386.deb

If you are a debian user, then just apt-get them.

good luck...

The usual Mac packages will follow in time, as usual there are a few
quirks with them.  I know Jason has this working so it should not be
that much of a problem.

Now, who was it out there who had volunteered to write a wiki page for
this if I made the package? :)


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From nikelski at bic.mni.mcgill.ca  Thu May 10 18:45:47 2007
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Thu, 10 May 2007 18:45:47 -0400
Subject: [MINC-users] brain-view binary (and source packages).
In-Reply-To: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
References: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
Message-ID: <e12172550705101545h3dfad4den1f361ebae9e0bef3@mail.gmail.com>

Hi all,

   Many thanks for the work Andrew, however, I believe I have a problem.
We're running Edgy, and I came across 3 problems: 2 solvable, and 1
definitely not.

Solvable 1: the pcre lib on Edgy seems to have a different name, thus a sym
lnk is necessary:
>>ln -s libpcrecpp.so.0.0.0 libpcre++.so.0

Sovable 2: missing simage lib.  So, need to install ...
>>apt-get install libsimage20c2

Unsolvable: Programs runs well, however aborts whenever I pick the pointy
tool and click on the cortical surface.  The output looks a little like this
..

...
adding texture
adding geometry
after callback registration
after cameras
after setting of scene graph
before showing of viewers
Just before loop  **** I initiate the problem right here ****
Picker - num points: 3
Picker - index: 27781
Picker - index: 27780
Picker - index: 6974
brain-view: symbol lookup error: brain-view: undefined symbol:
_ZN6pcrepp4PcreC1ERKSsS2_

Looks related to the pcre lib, don't I really don't understand entry point
mangling. Any ideas?

-Jim



On 5/10/07, Andrew Janke <a.janke at gmail.com> wrote:
>
> Finally I have this done,
>
> get it fresh from:
>
>    packages.bic.mni.mcgil.ca/deb
>
> or in source from
>
>    packages.bic.mni.mcgill.ca/tgz
>
> Note that this thing has a heap of dependencies that I have no
> included as pre-requisites in the package if only because I am sure
> there are a few versions of COIN and the likes out there.
>
> So, on my system (ubuntu feisty), I had to install these packages.
>
>    apt-get install libpcre3 libglut3 libxmu6 libxi6 libcoin40c2
> libqt3-mt libsoqt20
>
> once you have these and the packages line in your sources.list just type:
>
>    apt-get install brain-view
>
>
>
>
> ------
>
>
> Now if you want to build it from source (hey there are those out there
> who might like to).
>
> you will need to download these source packages from /tgz
>
>    arguments-0.2.1.tar.gz
>    bicInventor-0.3.1.tar.gz
>    oobicpl-0.4.3.tar.gz
>    brain-view-0.6.2.tar.gz
>
> and them make them in that order.  Of course you will also (if you are
> on a debian system have to install this lot:
>
>    apt-get install libpcre3-dev libglut3-dev libxmu-dev libxi-dev \
>       libcoin40-dev libqt3-mt-dev libsoqt-dev
>
> and you still wont be finished as then you will have to (if you are on
> ubuntu) go and get these:
>
>    libpcre++-dev_0.9.5-2_i386.deb
>    libpcre++0_0.9.5-2_i386.deb
>
> If you are a debian user, then just apt-get them.
>
> good luck...
>
> The usual Mac packages will follow in time, as usual there are a few
> quirks with them.  I know Jason has this working so it should not be
> that much of a problem.
>
> Now, who was it out there who had volunteered to write a wiki page for
> this if I made the package? :)
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University
Tel: (514) 340-8222 x 2298
Fax: (514) 340-8295

From vladimir.fonov at gmail.com  Thu May 10 20:26:00 2007
From: vladimir.fonov at gmail.com (Vladimir FONOV)
Date: Thu, 10 May 2007 20:26:00 -0400
Subject: [MINC-users] brain-view binary (and source packages).
In-Reply-To: <e12172550705101545h3dfad4den1f361ebae9e0bef3@mail.gmail.com>
References: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
	<e12172550705101545h3dfad4den1f361ebae9e0bef3@mail.gmail.com>
Message-ID: <ea3878950705101726i59c08fbax21ac013693dd776c@mail.gmail.com>

Hello Jim,

you wrote:
>
> Solvable 1: the pcre lib on Edgy seems to have a different name, thus a sym
> lnk is necessary:
> >>ln -s libpcrecpp.so.0.0.0 libpcre++.so.0

> Unsolvable: Programs runs well, however aborts whenever I pick the pointy
> tool and click on the cortical surface.  The output looks a little like this

> brain-view: symbol lookup error: brain-view: undefined symbol:
> _ZN6pcrepp4PcreC1ERKSsS2_
>
> Looks related to the pcre lib, don't I really don't understand entry point
> mangling. Any ideas?
Looks like it is the same problem, actually. Probably solution will be
to create ubuntu package based on the version of pcre++ supplied with
ubuntu. (Or compile from source)


-- 
Best regards,
 Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From a.janke at gmail.com  Thu May 10 21:53:26 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 11 May 2007 11:53:26 +1000
Subject: [MINC-users] brain-view binary (and source packages).
In-Reply-To: <ea3878950705101726i59c08fbax21ac013693dd776c@mail.gmail.com>
References: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
	<e12172550705101545h3dfad4den1f361ebae9e0bef3@mail.gmail.com>
	<ea3878950705101726i59c08fbax21ac013693dd776c@mail.gmail.com>
Message-ID: <d747ed50705101853o29a0613aj975acca43795e348@mail.gmail.com>

Hi Jim,

I dont think there is a pcre++ ubuntu package.  In my case I just
downloaded the pcre++ package from debian and installed that using
dpkg.

   http://packages.debian.org/unstable/libs/libpcre++0

worked for me, what I did find was that pcrecpp and pcre++ are
incompatible!  (been there tried that).

Perhaps I need to figure out how to include it statically, although
that will vbe somewhat problematic unless of course I include the
source in brain-view


a

On 5/11/07, Vladimir FONOV <vladimir.fonov at gmail.com> wrote:
> Hello Jim,
>
> you wrote:
> >
> > Solvable 1: the pcre lib on Edgy seems to have a different name, thus a sym
> > lnk is necessary:
> > >>ln -s libpcrecpp.so.0.0.0 libpcre++.so.0
>
> > Unsolvable: Programs runs well, however aborts whenever I pick the pointy
> > tool and click on the cortical surface.  The output looks a little like this
>
> > brain-view: symbol lookup error: brain-view: undefined symbol:
> > _ZN6pcrepp4PcreC1ERKSsS2_
> >
> > Looks related to the pcre lib, don't I really don't understand entry point
> > mangling. Any ideas?
> Looks like it is the same problem, actually. Probably solution will be
> to create ubuntu package based on the version of pcre++ supplied with
> ubuntu. (Or compile from source)
>
>
> --
> Best regards,
>  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From rezwang at yahoo.com  Fri May 11 08:50:28 2007
From: rezwang at yahoo.com (Rezwan Ghassemi)
Date: Fri, 11 May 2007 05:50:28 -0700 (PDT)
Subject: [MINC-users] edge detection algorithm
Message-ID: <552954.29880.qm@web30901.mail.mud.yahoo.com>

Hello, 
   
  I am using "mincblur" for edge detection that I think, is a gradient based Sobel edge detector? is that right? How can I detect the edges using Canny algorithm with mincblur?
   
  thanks
  Rezwan

       
---------------------------------
Luggage? GPS? Comic books? 
Check out fitting  gifts for grads at Yahoo! Search.

From a.janke at gmail.com  Fri May 11 08:54:48 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 11 May 2007 22:54:48 +1000
Subject: [MINC-users] edge detection algorithm
In-Reply-To: <552954.29880.qm@web30901.mail.mud.yahoo.com>
References: <552954.29880.qm@web30901.mail.mud.yahoo.com>
Message-ID: <d747ed50705110554s1f0e5efbh21a1fa56092af32c@mail.gmail.com>

Hi Rezwan,

if by "edge detection" you mean the _dxyz images this is just the
combination of the partial derivatives.

mincblur itself does not have code for edge detection beyond this but
you could easily modify the code (it uses a fourier transformation and
convolution for the blurring) to do what you want.  The code is in the
mni-autoreg package.

   packages.bic.mni.mcgill.ca/tgz


a

On 5/11/07, Rezwan Ghassemi <rezwang at yahoo.com> wrote:
> Hello,
>
>   I am using "mincblur" for edge detection that I think, is a gradient based Sobel edge detector? is that right? How can I detect the edges using Canny algorithm with mincblur?
>
>   thanks
>   Rezwan
>
>
> ---------------------------------
> Luggage? GPS? Comic books?
> Check out fitting  gifts for grads at Yahoo! Search.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From rezwang at yahoo.com  Fri May 11 09:01:03 2007
From: rezwang at yahoo.com (Rezwan Ghassemi)
Date: Fri, 11 May 2007 06:01:03 -0700 (PDT)
Subject: [MINC-users] edge detection algorithm
In-Reply-To: <d747ed50705110554s1f0e5efbh21a1fa56092af32c@mail.gmail.com>
Message-ID: <933713.92920.qm@web30913.mail.mud.yahoo.com>

Thanks Andrew, but which code in the package is it?

Andrew Janke <a.janke at gmail.com> wrote:  Hi Rezwan,

if by "edge detection" you mean the _dxyz images this is just the
combination of the partial derivatives.

mincblur itself does not have code for edge detection beyond this but
you could easily modify the code (it uses a fourier transformation and
convolution for the blurring) to do what you want. The code is in the
mni-autoreg package.

packages.bic.mni.mcgill.ca/tgz


a

On 5/11/07, Rezwan Ghassemi wrote:
> Hello,
>
> I am using "mincblur" for edge detection that I think, is a gradient based Sobel edge detector? is that right? How can I detect the edges using Canny algorithm with mincblur?
>
> thanks
> Rezwan
>
>
> ---------------------------------
> Luggage? GPS? Comic books?
> Check out fitting gifts for grads at Yahoo! Search.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia +61 (402) 700 883
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


       
---------------------------------
Be a better Heartthrob. Get better relationship answers from someone who knows.
Yahoo! Answers - Check it out. 

From a.janke at gmail.com  Fri May 11 10:07:37 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 12 May 2007 00:07:37 +1000
Subject: [MINC-users] edge detection algorithm
In-Reply-To: <933713.92920.qm@web30913.mail.mud.yahoo.com>
References: <d747ed50705110554s1f0e5efbh21a1fa56092af32c@mail.gmail.com>
	<933713.92920.qm@web30913.mail.mud.yahoo.com>
Message-ID: <d747ed50705110707j681aff78p984ef5ea4983f3ae@mail.gmail.com>

Take a recent release of mni-autoreg and when you untar you will see a
drectory called mincblur.


a

On 5/11/07, Rezwan Ghassemi <rezwang at yahoo.com> wrote:
> Thanks Andrew, but which code in the package is it?
>
> Andrew Janke <a.janke at gmail.com> wrote:  Hi Rezwan,
>
> if by "edge detection" you mean the _dxyz images this is just the
> combination of the partial derivatives.
>
> mincblur itself does not have code for edge detection beyond this but
> you could easily modify the code (it uses a fourier transformation and
> convolution for the blurring) to do what you want. The code is in the
> mni-autoreg package.
>
> packages.bic.mni.mcgill.ca/tgz
>
>
> a
>
> On 5/11/07, Rezwan Ghassemi wrote:
> > Hello,
> >
> > I am using "mincblur" for edge detection that I think, is a gradient based Sobel edge detector? is that right? How can I detect the edges using Canny algorithm with mincblur?
> >
> > thanks
> > Rezwan
> >
> >
> > ---------------------------------
> > Luggage? GPS? Comic books?
> > Check out fitting gifts for grads at Yahoo! Search.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
>
> ---------------------------------
> Be a better Heartthrob. Get better relationship answers from someone who knows.
> Yahoo! Answers - Check it out.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From nikelski at bic.mni.mcgill.ca  Fri May 11 11:20:47 2007
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Fri, 11 May 2007 11:20:47 -0400
Subject: [MINC-users] brain-view binary (and source packages).
In-Reply-To: <d747ed50705101853o29a0613aj975acca43795e348@mail.gmail.com>
References: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
	<e12172550705101545h3dfad4den1f361ebae9e0bef3@mail.gmail.com>
	<ea3878950705101726i59c08fbax21ac013693dd776c@mail.gmail.com>
	<d747ed50705101853o29a0613aj975acca43795e348@mail.gmail.com>
Message-ID: <e12172550705110820xb7e25c5gdec0015254c0cfa3@mail.gmail.com>

Hi,

   Thanks Andrew. I installed the Debian unstable pcre++ package, which
solves the immediate abort problem.  Initial testing has yielded a seg fault
after a couple of minutes of clicking about on the cortical surface. If I
have time, I'll fire up gdb and take a peek.

-Jim



On 5/10/07, Andrew Janke <a.janke at gmail.com> wrote:
>
> Hi Jim,
>
> I dont think there is a pcre++ ubuntu package.  In my case I just
> downloaded the pcre++ package from debian and installed that using
> dpkg.
>
>    http://packages.debian.org/unstable/libs/libpcre++0
>
> worked for me, what I did find was that pcrecpp and pcre++ are
> incompatible!  (been there tried that).
>
> Perhaps I need to figure out how to include it statically, although
> that will vbe somewhat problematic unless of course I include the
> source in brain-view
>
>
> a
>
> On 5/11/07, Vladimir FONOV <vladimir.fonov at gmail.com> wrote:
> > Hello Jim,
> >
> > you wrote:
> > >
> > > Solvable 1: the pcre lib on Edgy seems to have a different name, thus
> a sym
> > > lnk is necessary:
> > > >>ln -s libpcrecpp.so.0.0.0 libpcre++.so.0
> >
> > > Unsolvable: Programs runs well, however aborts whenever I pick the
> pointy
> > > tool and click on the cortical surface.  The output looks a little
> like this
> >
> > > brain-view: symbol lookup error: brain-view: undefined symbol:
> > > _ZN6pcrepp4PcreC1ERKSsS2_
> > >
> > > Looks related to the pcre lib, don't I really don't understand entry
> point
> > > mangling. Any ideas?
> > Looks like it is the same problem, actually. Probably solution will be
> > to create ubuntu package based on the version of pcre++ supplied with
> > ubuntu. (Or compile from source)
> >
> >
> > --
> > Best regards,
> >  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University
Tel: (514) 340-8222 x 2298
Fax: (514) 340-8295

From se at hst.aau.dk  Sun May 13 08:23:57 2007
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Sun, 13 May 2007 14:23:57 +0200
Subject: [MINC-users] minctracc angles problem
Message-ID: <4647035D.9080301@hst.aau.dk>

Hi all,

I run
minctracc -lsq12 -mi input.mnc target.mnc output.xfm

and get:
COG of v1: -0.014192 136.356400 -4.679813
COG of v2: 0.591960 -18.756006 3.126583
    [trans] = 0.606151 -155.112411 7.806396
WARNING: (rotmat_to_ang.c:187) step one: rz not in the range -pi/2..pi/2
Could not extract angles from rotation matrix:
   -0.711324    0.703226    0.030620
    0.703189    0.714539    0.039374
    0.036176    0.026770    1.002540
You can try rerunning minctracc with '-est_translation'
The program will continue with angles = 0.0, 0.0, 0.0

I guess it means that no rotations are performed. Why does minctracc not 
handle rotations outside the range -pi/2..pi/2 ?
Is there a way to solve this. Running with -est_translation does not 
solve anything.

Thanks,
Simon

From a.janke at gmail.com  Sun May 13 08:33:24 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 13 May 2007 22:33:24 +1000
Subject: [MINC-users] minctracc angles problem
In-Reply-To: <4647035D.9080301@hst.aau.dk>
References: <4647035D.9080301@hst.aau.dk>
Message-ID: <d747ed50705130533h4e6e96d4t31bc797a4bb46f81@mail.gmail.com>

> I run
> minctracc -lsq12 -mi input.mnc target.mnc output.xfm
>
> and get:
> COG of v1: -0.014192 136.356400 -4.679813
> COG of v2: 0.591960 -18.756006 3.126583
>     [trans] = 0.606151 -155.112411 7.806396
> WARNING: (rotmat_to_ang.c:187) step one: rz not in the range -pi/2..pi/2
> Could not extract angles from rotation matrix:
>    -0.711324    0.703226    0.030620
>     0.703189    0.714539    0.039374
>     0.036176    0.026770    1.002540
> You can try rerunning minctracc with '-est_translation'
> The program will continue with angles = 0.0, 0.0, 0.0
>
> I guess it means that no rotations are performed.

It means that you have a rotation matrix that cannot be decomposed
(sensibly) into Euler angles in the range you say below.  This matrix
is defined in the inital setup of a minctracc alignment.  Occasionally
this pre-processing step doesn't do so well thus the suggestion to
start with zero rotation.

Once this setup of the rotations is complete, minctracc goes onto
simplex optimisation of the Euler Angles.

> Why does minctracc not
> handle rotations outside the range -pi/2..pi/2 ?

Because it optimises (using simplex) with Euler angles.  These only
make sense in this range otherwise you will get into problems such as
"gimball lock", one of the big drawbacks of a Euler angle
decomposition.

> Is there a way to solve this. Running with -est_translation does not
> solve anything.

try -identity... ;)

Either that or there is some experimental code in there that uses
quaternions in stead of Euler Angles for the optimisation, this is not
limited to rotations of pi/2.  To use it I would suggest the following

   minctracc -quaternions -identity

I think wikipedia has a good Euler angles vs quaternion thingo, I know
mathworld does but it s rather "mathy". the simple way to think of it
is:

   Euler angles: 3 rotations with a rotating frame of reference

   Quaternions: an axis (3 parameters) And a rotation.
        -- NOTE! this is not the 4 numbers you see! but can be obtained from
            them easily.


Side note: quaternions are what is used in most games to rotate
things...  the ubiquitous drag and drop for rotation as is used in
viewnup.

a



-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From se at hst.aau.dk  Sun May 13 10:00:31 2007
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Sun, 13 May 2007 16:00:31 +0200
Subject: [MINC-users] minctracc angles problem
In-Reply-To: <d747ed50705130533h4e6e96d4t31bc797a4bb46f81@mail.gmail.com>
References: <4647035D.9080301@hst.aau.dk>
	<d747ed50705130533h4e6e96d4t31bc797a4bb46f81@mail.gmail.com>
Message-ID: <464719FF.8080205@hst.aau.dk>

Andrew Janke wrote:
> try -identity... ;)
Well...identity is not an option in this case :-/

> Either that or there is some experimental code in there that uses
> quaternions in stead of Euler Angles for the optimisation, this is not
> limited to rotations of pi/2.  To use it I would suggest the following
> 
>    minctracc -quaternions -identity
The quaternions do not seem to do a better job (if any change at all).

I ended up providing a rough transformation as initial guess, which put 
the source within the pi/2 range of target.

Best,
Simon

From a.janke at gmail.com  Tue May 15 12:37:26 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 16 May 2007 02:37:26 +1000
Subject: [MINC-users] Release of a few scripts
Message-ID: <d747ed50705150937k7ae50c4bu316585cc72ae6fff@mail.gmail.com>

Hi all,

I have started to put a number of the scripts that I have written from
time to time here:

    http://packages.bic.mni.mcgill.ca/scripts

Currently there are three there, I hope to add more as time goes by.
(I dont count ana2mnc as worthy anymore).

   nlpfit - a generalised script that I use for nonlinear fitting.

   xfmavg - averages a series of xfm files together

   xfmflip - flips an xfm about the x, y, or z axes

They are of course not officially supported but I would be interested
to know if they are useful to others, if so I will put time into
making more available.


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From vladimir.fonov at gmail.com  Tue May 15 13:29:09 2007
From: vladimir.fonov at gmail.com (Vladimir FONOV)
Date: Tue, 15 May 2007 13:29:09 -0400
Subject: [MINC-users] Release of a few scripts
In-Reply-To: <d747ed50705150937k7ae50c4bu316585cc72ae6fff@mail.gmail.com>
References: <d747ed50705150937k7ae50c4bu316585cc72ae6fff@mail.gmail.com>
Message-ID: <ea3878950705151029ga831f68sad1684d535d28521@mail.gmail.com>

Hello,

On 5/15/07, Andrew Janke <a.janke at gmail.com> wrote:
> Hi all,
>
> I have started to put a number of the scripts that I have written from
> time to time here:
>
>     http://packages.bic.mni.mcgill.ca/scripts
>
> Currently there are three there, I hope to add more as time goes by.
> (I dont count ana2mnc as worthy anymore).
>
>    nlpfit - a generalised script that I use for nonlinear fitting.
>
>    xfmavg - averages a series of xfm files together
>
>    xfmflip - flips an xfm about the x, y, or z axes
>
How about bestlinreg from Claude ? Allso, his version of the nlpfit
(which does masking before blurring).


-- 
Best regards,
 Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From penhunelab at gmail.com  Tue May 15 14:27:11 2007
From: penhunelab at gmail.com (Penhune Lab)
Date: Tue, 15 May 2007 14:27:11 -0400
Subject: [MINC-users] mexmaci Files
Message-ID: <c983d2410705151127r1cd08938g32bf648d2bd1a361@mail.gmail.com>

Hi everybody

im trying to compile emma in an intel mac to use fmristat; however, im
encountering some problems. The compilation works fine, make install fine.
But when i go to matlab and call one of the .mexmaci files (like miinquire)
matlab closes, i dont get any error dialogs or anything, it just closes.
>From running it from a terminal i got to see the error:

penhune-lab-172-109:/Applications/MATLAB74/bin VP$ sudo ./matlab
terminate called after throwing an instance of
'MathWorks::System::_utException'
Abort trap

i thought it was a permissions error, thats why i sudo'ed it, but it seems
to be more of a problem in the compiled mexmac files.
has anyone ever experienced this before??

as a last resort, is there a precompiled version of emma?

im using mac os 10.4.9 and
matlab 2007a

thanks,

Alejandro Endo


-- 
Laboratory for Motor Learning and Neural Plasticity
Dr. Virginia Penhune
Department of Psychology, Concordia University
SP-A 244, 7141 Sherbrooke St. W
Montreal, QC  H4B 1R6  Canada
(514)848-2424 ext. 7567
http://psychology.concordia.ca/fac/penhune/winindex.html

From alex at bic.mni.mcgill.ca  Tue May 15 15:16:24 2007
From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS)
Date: Tue, 15 May 2007 15:16:24 -0400
Subject: [MINC-users] minc/debian/GLIBC_2_4?
Message-ID: <20070515151624.A17043659@bic.mni.mcgill.ca>

Hallo all,

I've been scratching my head on this one for a while now, and I'm
still stuck. I have a MINC installation on a debian sarge machine
which used to work fine and is suddenly broken:

$ mincinfo -help
mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)

My (so far unconfirmed) suspicion is that this happened the last time
I ran apt-get update/upgrade, which installed

  libc6 2.3.2.ds1-22sarge6

the previous version was either -sarge4 or -sarge5

Anybody else run into this? 

Thanks,

-- Alex


From Jean-Francois.Malouin at bic.mni.mcgill.ca  Tue May 15 15:21:43 2007
From: Jean-Francois.Malouin at bic.mni.mcgill.ca (Jean-Francois Malouin)
Date: Tue, 15 May 2007 15:21:43 -0400
Subject: [MINC-users] minc/debian/GLIBC_2_4?
In-Reply-To: <20070515151624.A17043659@bic.mni.mcgill.ca>
References: <20070515151624.A17043659@bic.mni.mcgill.ca>
Message-ID: <20070515192142.GA16760605@yorick.bic.mni.mcgill.ca>

* Alex ZIJDENBOS <alex at bic.mni.mcgill.ca> [20070515 15:16]:
> Hallo all,
> 
> I've been scratching my head on this one for a while now, and I'm
> still stuck. I have a MINC installation on a debian sarge machine
> which used to work fine and is suddenly broken:
> 
> $ mincinfo -help
> mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)
> 
> My (so far unconfirmed) suspicion is that this happened the last time
> I ran apt-get update/upgrade, which installed
> 
>   libc6 2.3.2.ds1-22sarge6
> 
> the previous version was either -sarge4 or -sarge5
> 
> Anybody else run into this? 

Yes.
We are busy distributing the stars at the moment...
Stay tuned.

jf

> 
> Thanks,
> 
> -- Alex
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

-- 
<? ><

From sylvain at bic.mni.mcgill.ca  Tue May 15 15:37:19 2007
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Tue, 15 May 2007 15:37:19 -0400
Subject: [MINC-users] minc/debian/GLIBC_2_4?
In-Reply-To: <20070515151624.A17043659@bic.mni.mcgill.ca>
References: <20070515151624.A17043659@bic.mni.mcgill.ca>
Message-ID: <Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>


Hi ALex,

well I just checked, this is not one of our systems as they all have minc
1.4. (well actually, until this morning, all but one - this is now fixed)
I suspect you're running minc 1.5.1 which was released by Andrew and
made its way to the "apt" repository, and shouldn't have, but has now been
removed. If you're sourcing stuff from packages.bic.mni.mcgill.ca, you
will get version 1.5.1 and also if you sourced from /mirror/mni-packages
between May 10th and this morning.

As for why mincinfo version 1.5.1 is broken, ask Andrew.

S


 On Tue, 15 May 2007, Alex ZIJDENBOS wrote:

> Hallo all,
>
> I've been scratching my head on this one for a while now, and I'm
> still stuck. I have a MINC installation on a debian sarge machine
> which used to work fine and is suddenly broken:
>
> $ mincinfo -help
> mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)
>
> My (so far unconfirmed) suspicion is that this happened the last time
> I ran apt-get update/upgrade, which installed
>
>   libc6 2.3.2.ds1-22sarge6
>
> the previous version was either -sarge4 or -sarge5
>
> Anybody else run into this?
>
> Thanks,
>
> -- Alex
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (bicadmin at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4

From alex at bic.mni.mcgill.ca  Tue May 15 15:41:35 2007
From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS)
Date: Tue, 15 May 2007 15:41:35 -0400
Subject: [MINC-users] minc/debian/GLIBC_2_4?
In-Reply-To: <Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>;
	from sylvain@bic.mni.mcgill.ca on Tue, May 15, 2007 at 03:37:19PM
	-0400
References: <20070515151624.A17043659@bic.mni.mcgill.ca>
	<Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>
Message-ID: <20070515154135.A17115080@bic.mni.mcgill.ca>

It is true, I was not talking about a BIC system (hence I posted to
minc-users and not a local bic list :)

However, I do know that it is not related to minc 1.5.1. This problem
occurred with minc 1.4, then I upgraded minc and got 1.5.1, and the
problem remained.

-- A

On Tue, May 15, 2007 at 03:37:19PM -0400, Sylvain MILOT wrote:
> 
> Hi ALex,
> 
> well I just checked, this is not one of our systems as they all have minc
> 1.4. (well actually, until this morning, all but one - this is now fixed)
> I suspect you're running minc 1.5.1 which was released by Andrew and
> made its way to the "apt" repository, and shouldn't have, but has now been
> removed. If you're sourcing stuff from packages.bic.mni.mcgill.ca, you
> will get version 1.5.1 and also if you sourced from /mirror/mni-packages
> between May 10th and this morning.
> 
> As for why mincinfo version 1.5.1 is broken, ask Andrew.
> 
> S
> 
> 
>  On Tue, 15 May 2007, Alex ZIJDENBOS wrote:
> 
> > Hallo all,
> >
> > I've been scratching my head on this one for a while now, and I'm
> > still stuck. I have a MINC installation on a debian sarge machine
> > which used to work fine and is suddenly broken:
> >
> > $ mincinfo -help
> > mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)
> >
> > My (so far unconfirmed) suspicion is that this happened the last time
> > I ran apt-get update/upgrade, which installed
> >
> >   libc6 2.3.2.ds1-22sarge6
> >
> > the previous version was either -sarge4 or -sarge5
> >
> > Anybody else run into this?
> >
> > Thanks,
> >
> > -- Alex
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> 
> ---
> Sylvain Milot (sylvain at bic.mni.mcgill.ca)
>               (bicadmin at bic.mni.mcgill.ca)
> Brain Imaging Centre
> Montreal Neurological Institute
> 3801 University Street
> Webster 2B, Room 208
> Montreal, Qc., Canada, H3A 2B4
> Phone  : (514) 398-4965, Fax: 398-8948
> Mobile : (514) 712-1768
> Office : 527 Av Des Pins O., Room 204
>          Montreal, Qc., H2W 1S4
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

-- 
=========================================================================
| Alex P. Zijdenbos, Ph.D.        |                                     |
| McConnell Brain Imaging Centre  |  Phone: [+1] 514 398-5220  (office) |
| Montreal Neurological Institute |         [+1] 514 398-1996   (dept.) |
| 3801 University St., WB-208     |    Fax: [+1] 514 398-8952  (office) |
| Montreal, Quebec, H3A 2B4       |         [+1] 708 810-3309 (private) | 
| CANADA                          | E-mail:      alex at bic.mni.mcgill.ca |
=========================================================================


From acveilleux at mrs.mni.mcgill.ca  Tue May 15 15:47:25 2007
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Tue, 15 May 2007 15:47:25 -0400
Subject: [MINC-users] minc/debian/GLIBC_2_4?
In-Reply-To: <Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>;
	from sylvain@bic.mni.mcgill.ca on Tue, May 15, 2007 at 03:37:19PM
	-0400
References: <20070515151624.A17043659@bic.mni.mcgill.ca>
	<Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>
Message-ID: <20070515154725.B798@mrs.mni.mcgill.ca>

	A quick point: Debian sarge should never have glibc/libc6 2.4 to
begin with. Was a Ubuntu libc6 binary installed in /lib somewhere?

	Also, why in the name of all things holy is libc6 in /lib/tls? Do
you have multiple libc's installed or a bug in your ld.so/lib config?

Alex

	
On Tue, May 15, 2007 at 03:37:19PM -0400, Sylvain MILOT wrote:
> Date: Tue, 15 May 2007 15:37:19 -0400
> From: Sylvain MILOT <sylvain at bic.mni.mcgill.ca>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] minc/debian/GLIBC_2_4?
> 
> 
> Hi ALex,
> 
> well I just checked, this is not one of our systems as they all have minc
> 1.4. (well actually, until this morning, all but one - this is now fixed)
> I suspect you're running minc 1.5.1 which was released by Andrew and
> made its way to the "apt" repository, and shouldn't have, but has now been
> removed. If you're sourcing stuff from packages.bic.mni.mcgill.ca, you
> will get version 1.5.1 and also if you sourced from /mirror/mni-packages
> between May 10th and this morning.
> 
> As for why mincinfo version 1.5.1 is broken, ask Andrew.
> 
> S
> 
> 
>  On Tue, 15 May 2007, Alex ZIJDENBOS wrote:
> 
> > Hallo all,
> >
> > I've been scratching my head on this one for a while now, and I'm
> > still stuck. I have a MINC installation on a debian sarge machine
> > which used to work fine and is suddenly broken:
> >
> > $ mincinfo -help
> > mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)
> >
> > My (so far unconfirmed) suspicion is that this happened the last time
> > I ran apt-get update/upgrade, which installed
> >
> >   libc6 2.3.2.ds1-22sarge6
> >
> > the previous version was either -sarge4 or -sarge5
> >
> > Anybody else run into this?
> >
> > Thanks,
> >
> > -- Alex
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> 
> ---
> Sylvain Milot (sylvain at bic.mni.mcgill.ca)
>               (bicadmin at bic.mni.mcgill.ca)
> Brain Imaging Centre
> Montreal Neurological Institute
> 3801 University Street
> Webster 2B, Room 208
> Montreal, Qc., Canada, H3A 2B4
> Phone  : (514) 398-4965, Fax: 398-8948
> Mobile : (514) 712-1768
> Office : 527 Av Des Pins O., Room 204
>          Montreal, Qc., H2W 1S4
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From alex at bic.mni.mcgill.ca  Tue May 15 15:51:24 2007
From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS)
Date: Tue, 15 May 2007 15:51:24 -0400
Subject: [MINC-users] minc/debian/GLIBC_2_4?
In-Reply-To: <20070515154135.A17115080@bic.mni.mcgill.ca>;
	from alex@bic.mni.mcgill.ca on Tue, May 15, 2007 at 03:41:35PM
	-0400
References: <20070515151624.A17043659@bic.mni.mcgill.ca>
	<Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>
	<20070515154135.A17115080@bic.mni.mcgill.ca>
Message-ID: <20070515155124.A16913224@bic.mni.mcgill.ca>

Actually I retract my second comment, I didn't quite follow my own
series of experiments correctly :) I downgraded to minc-1.4 and all is
well again - so the problem appears indeed to be with minc-1.5.1.

-- A

On Tue, May 15, 2007 at 03:41:35PM -0400, Alex ZIJDENBOS wrote:
> It is true, I was not talking about a BIC system (hence I posted to
> minc-users and not a local bic list :)
> 
> However, I do know that it is not related to minc 1.5.1. This problem
> occurred with minc 1.4, then I upgraded minc and got 1.5.1, and the
> problem remained.
> 
> -- A
> 
> On Tue, May 15, 2007 at 03:37:19PM -0400, Sylvain MILOT wrote:
> > 
> > Hi ALex,
> > 
> > well I just checked, this is not one of our systems as they all have minc
> > 1.4. (well actually, until this morning, all but one - this is now fixed)
> > I suspect you're running minc 1.5.1 which was released by Andrew and
> > made its way to the "apt" repository, and shouldn't have, but has now been
> > removed. If you're sourcing stuff from packages.bic.mni.mcgill.ca, you
> > will get version 1.5.1 and also if you sourced from /mirror/mni-packages
> > between May 10th and this morning.
> > 
> > As for why mincinfo version 1.5.1 is broken, ask Andrew.
> > 
> > S
> > 
> > 
> >  On Tue, 15 May 2007, Alex ZIJDENBOS wrote:
> > 
> > > Hallo all,
> > >
> > > I've been scratching my head on this one for a while now, and I'm
> > > still stuck. I have a MINC installation on a debian sarge machine
> > > which used to work fine and is suddenly broken:
> > >
> > > $ mincinfo -help
> > > mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)
> > >
> > > My (so far unconfirmed) suspicion is that this happened the last time
> > > I ran apt-get update/upgrade, which installed
> > >
> > >   libc6 2.3.2.ds1-22sarge6
> > >
> > > the previous version was either -sarge4 or -sarge5
> > >
> > > Anybody else run into this?
> > >
> > > Thanks,
> > >
> > > -- Alex
> > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > 
> > ---
> > Sylvain Milot (sylvain at bic.mni.mcgill.ca)
> >               (bicadmin at bic.mni.mcgill.ca)
> > Brain Imaging Centre
> > Montreal Neurological Institute
> > 3801 University Street
> > Webster 2B, Room 208
> > Montreal, Qc., Canada, H3A 2B4
> > Phone  : (514) 398-4965, Fax: 398-8948
> > Mobile : (514) 712-1768
> > Office : 527 Av Des Pins O., Room 204
> >          Montreal, Qc., H2W 1S4
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
> -- 
> =========================================================================
> | Alex P. Zijdenbos, Ph.D.        |                                     |
> | McConnell Brain Imaging Centre  |  Phone: [+1] 514 398-5220  (office) |
> | Montreal Neurological Institute |         [+1] 514 398-1996   (dept.) |
> | 3801 University St., WB-208     |    Fax: [+1] 514 398-8952  (office) |
> | Montreal, Quebec, H3A 2B4       |         [+1] 708 810-3309 (private) | 
> | CANADA                          | E-mail:      alex at bic.mni.mcgill.ca |
> =========================================================================
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

-- 
=========================================================================
| Alex P. Zijdenbos, Ph.D.        |                                     |
| McConnell Brain Imaging Centre  |  Phone: [+1] 514 398-5220  (office) |
| Montreal Neurological Institute |         [+1] 514 398-1996   (dept.) |
| 3801 University St., WB-208     |    Fax: [+1] 514 398-8952  (office) |
| Montreal, Quebec, H3A 2B4       |         [+1] 708 810-3309 (private) | 
| CANADA                          | E-mail:      alex at bic.mni.mcgill.ca |
=========================================================================


From alex at bic.mni.mcgill.ca  Tue May 15 16:00:24 2007
From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS)
Date: Tue, 15 May 2007 16:00:24 -0400
Subject: [MINC-users] minc/debian/GLIBC_2_4?
In-Reply-To: <20070515154725.B798@mrs.mni.mcgill.ca>;
	from acveilleux@mrs.mni.mcgill.ca on Tue, May 15, 2007 at
	03:47:25PM -0400
References: <20070515151624.A17043659@bic.mni.mcgill.ca>
	<Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>
	<20070515154725.B798@mrs.mni.mcgill.ca>
Message-ID: <20070515160024.B16913224@bic.mni.mcgill.ca>

On Tue, May 15, 2007 at 03:47:25PM -0400, Alexandre CARMEL-VEILLEUX wrote:
> 	A quick point: Debian sarge should never have glibc/libc6 2.4 to
> begin with. Was a Ubuntu libc6 binary installed in /lib somewhere?

I think the problem is that minc-1.5.1 seems to want 2.4, which indeed
is not partof sarge (I currently have 2.3.2.ds1-22sarge6).

> 	Also, why in the name of all things holy is libc6 in /lib/tls? Do
> you have multiple libc's installed or a bug in your ld.so/lib config?

Nope, that dir is part of the libc6 package:

# dpkg -L libc6  | grep tls | grep libc
/lib/tls/libc-2.3.2.so
/lib/tls/libcrypt-2.3.2.so
/lib/tls/libcrypt.so.1
/lib/tls/libc.so.6

> Alex

Ditto

> 
> 	
> On Tue, May 15, 2007 at 03:37:19PM -0400, Sylvain MILOT wrote:
> > Date: Tue, 15 May 2007 15:37:19 -0400
> > From: Sylvain MILOT <sylvain at bic.mni.mcgill.ca>
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-users] minc/debian/GLIBC_2_4?
> > 
> > 
> > Hi ALex,
> > 
> > well I just checked, this is not one of our systems as they all have minc
> > 1.4. (well actually, until this morning, all but one - this is now fixed)
> > I suspect you're running minc 1.5.1 which was released by Andrew and
> > made its way to the "apt" repository, and shouldn't have, but has now been
> > removed. If you're sourcing stuff from packages.bic.mni.mcgill.ca, you
> > will get version 1.5.1 and also if you sourced from /mirror/mni-packages
> > between May 10th and this morning.
> > 
> > As for why mincinfo version 1.5.1 is broken, ask Andrew.
> > 
> > S
> > 
> > 
> >  On Tue, 15 May 2007, Alex ZIJDENBOS wrote:
> > 
> > > Hallo all,
> > >
> > > I've been scratching my head on this one for a while now, and I'm
> > > still stuck. I have a MINC installation on a debian sarge machine
> > > which used to work fine and is suddenly broken:
> > >
> > > $ mincinfo -help
> > > mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)
> > >
> > > My (so far unconfirmed) suspicion is that this happened the last time
> > > I ran apt-get update/upgrade, which installed
> > >
> > >   libc6 2.3.2.ds1-22sarge6
> > >
> > > the previous version was either -sarge4 or -sarge5
> > >
> > > Anybody else run into this?
> > >
> > > Thanks,
> > >
> > > -- Alex
> > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > 
> > ---
> > Sylvain Milot (sylvain at bic.mni.mcgill.ca)
> >               (bicadmin at bic.mni.mcgill.ca)
> > Brain Imaging Centre
> > Montreal Neurological Institute
> > 3801 University Street
> > Webster 2B, Room 208
> > Montreal, Qc., Canada, H3A 2B4
> > Phone  : (514) 398-4965, Fax: 398-8948
> > Mobile : (514) 712-1768
> > Office : 527 Av Des Pins O., Room 204
> >          Montreal, Qc., H2W 1S4
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

-- 
=========================================================================
| Alex P. Zijdenbos, Ph.D.        |                                     |
| McConnell Brain Imaging Centre  |  Phone: [+1] 514 398-5220  (office) |
| Montreal Neurological Institute |         [+1] 514 398-1996   (dept.) |
| 3801 University St., WB-208     |    Fax: [+1] 514 398-8952  (office) |
| Montreal, Quebec, H3A 2B4       |         [+1] 708 810-3309 (private) | 
| CANADA                          | E-mail:      alex at bic.mni.mcgill.ca |
=========================================================================


From penhunelab at gmail.com  Wed May 16 10:57:29 2007
From: penhunelab at gmail.com (Penhune Lab)
Date: Wed, 16 May 2007 10:57:29 -0400
Subject: [MINC-users] Problem Buliding MNI Models
In-Reply-To: <d747ed50606040008o173839a9v17b1210e0335e172@mail.gmail.com>
References: <9c80f12d0605111036g56b5558i6b3b239bade6a326@mail.gmail.com>
	<d747ed50605162337l1cb4ea22ud460c2baaf696c6a@mail.gmail.com>
	<9c80f12d0605180839q20dd972fve6c16461cb392e96@mail.gmail.com>
	<d747ed50606040008o173839a9v17b1210e0335e172@mail.gmail.com>
Message-ID: <c983d2410705160757y1459a3e3je468ff4d0f8af78c@mail.gmail.com>

sorry to resurrect such an old thread but im having the same problem
building the models in an intel mac, getting the same errors:

[2006-05-11 13:31:55] /usr/local/bin/mincresample -clobber
icbm_avg_152_t1_tal_lin.mnc icbm_avg_152_t1_tal_lin_pad.mnc -start
-106 -142 -88 -step 2 2 2 -nelements 107 125 107Transforming
slices:...........................................................................................................Done
(from miopen): Can't write compressed file
ncredef: ncid -1: Not a netCDF id
ncattput: ncid -1: Not a netCDF id
ncclose: ncid -1: Not a netCDF id


the only difference is im using minc 2.0.11 as opposed to .10

im sure someone must have solved this problem since this is a fairly
necessary installation; any ideas how to fix this?? Andrew mentioned
something about minc not handling compression correctly, can i disable
compression?? i will try to modify the source code and will post a patch if
i succeed

Thank you very much,

Alejandro Endo

On 6/4/06, Andrew Janke <a.janke at gmail.com> wrote:
>
> Hi again Gil,
>
> Sorry about the late reply with this, but I just realised that you
> were using MINC 2.0.10.  There are a few "issues" in that release with
> respect to compression. I woud still suggest that if you are using
> MINC in a runtime environment to stick with minc 1.x (1.4 at this
> stage).
>
> MINC 2.0 is progressing slowly towards stability but there are still a
> few lingering issues.
>
>
> a
>
> On 5/18/06, Gil Citro <citrog at gmail.com> wrote:
> > Actually no, I compiled MINC 2.0.10 myself from the source.  I also
> > compiled NetCDF 3.6.1 from source, because NetCDF 3.5.0 would not
> > compile on my system.  Any suggestions for how to make NetCDF find
> > gzip?  Thanks again.
> >
> > Gil
> >
> > On 5/17/06, Andrew Janke <a.janke at gmail.com> wrote:
> >
> > >
> > > Looks like netcdf cannot find the gzip runtime libraries (to
> > > uncompress the input file).  If this minc install came from a binary
> > > package this would be suprising as they are supposed to be compiled
> > > static.
> > >
> > > On 5/11/06, Gil Citro <citrog at gmail.com> wrote:
> > > > I'm having trouble building and installing
> > > >
> > > > mni-models_average305-lin-1.0
> > > > mni-models_colin27-lin-1.0
> > > > mni-models_icbm152-lin-1.0
> > > >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canada->Montreal                                   Cell: +1 (514) 924 2012
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Laboratory for Motor Learning and Neural Plasticity directed by
Dr. Virginia Penhune
Department of Psychology, Concordia University
SP-A 244, 7141 Sherbrooke St. W
Montreal, QC  H4B 1R6  Canada
(514)848-2424 ext. 7567
http://psychology.concordia.ca/fac/penhune/winindex.html

From mferre at bic.mni.mcgill.ca  Wed May 16 15:49:17 2007
From: mferre at bic.mni.mcgill.ca (Michael Ferreira)
Date: Wed, 16 May 2007 15:49:17 -0400
Subject: [MINC-users] mexmaci Files
In-Reply-To: <c983d2410705151127r1cd08938g32bf648d2bd1a361@mail.gmail.com>
References: <c983d2410705151127r1cd08938g32bf648d2bd1a361@mail.gmail.com>
Message-ID: <464B603D.7000905@bic.mni.mcgill.ca>

Hello Alejandro,

I have installed emma version 0.9.8 and it runs fine on my system (also 
10.4.9/Matlab 2007a).

There is no pre-compiled version for mac that I know of.  But I can 
e-mail you my toolbox directory.

Regards,

mike

Penhune Lab wrote:
> Hi everybody
> 
> im trying to compile emma in an intel mac to use fmristat; however, im
> encountering some problems. The compilation works fine, make install fine.
> But when i go to matlab and call one of the .mexmaci files (like miinquire)
> matlab closes, i dont get any error dialogs or anything, it just closes.
>>From running it from a terminal i got to see the error:
> 
> penhune-lab-172-109:/Applications/MATLAB74/bin VP$ sudo ./matlab
> terminate called after throwing an instance of
> 'MathWorks::System::_utException'
> Abort trap
> 
> i thought it was a permissions error, thats why i sudo'ed it, but it seems
> to be more of a problem in the compiled mexmac files.
> has anyone ever experienced this before??
> 
> as a last resort, is there a precompiled version of emma?
> 
> im using mac os 10.4.9 and
> matlab 2007a
> 
> thanks,
> 
> Alejandro Endo
> 
> 

From a.janke at gmail.com  Thu May 17 10:15:54 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 18 May 2007 00:15:54 +1000
Subject: [MINC-users] minc/debian/GLIBC_2_4?
In-Reply-To: <20070515154725.B798@mrs.mni.mcgill.ca>
References: <20070515151624.A17043659@bic.mni.mcgill.ca>
	<Pine.SGI.4.58.0705151526240.17056693@yorick.bic.mni.mcgill.ca>
	<20070515154725.B798@mrs.mni.mcgill.ca>
Message-ID: <d747ed50705170715g7e5c454cu1c6966474bb2c61a@mail.gmail.com>

Well you are all close..  I copied the MINC 1.5.1 binary from my
Ubuntu build to /deb on packages.  That was a whoopsie (sorry).

I will rebuild the debian (Stable) version shortly.


a


On 16/05/07, Alexandre CARMEL-VEILLEUX <acveilleux at mrs.mni.mcgill.ca> wrote:
>         A quick point: Debian sarge should never have glibc/libc6 2.4 to
> begin with. Was a Ubuntu libc6 binary installed in /lib somewhere?
>
>         Also, why in the name of all things holy is libc6 in /lib/tls? Do
> you have multiple libc's installed or a bug in your ld.so/lib config?
>
> Alex
>
>
> On Tue, May 15, 2007 at 03:37:19PM -0400, Sylvain MILOT wrote:
> > Date: Tue, 15 May 2007 15:37:19 -0400
> > From: Sylvain MILOT <sylvain at bic.mni.mcgill.ca>
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > Subject: Re: [MINC-users] minc/debian/GLIBC_2_4?
> >
> >
> > Hi ALex,
> >
> > well I just checked, this is not one of our systems as they all have minc
> > 1.4. (well actually, until this morning, all but one - this is now fixed)
> > I suspect you're running minc 1.5.1 which was released by Andrew and
> > made its way to the "apt" repository, and shouldn't have, but has now been
> > removed. If you're sourcing stuff from packages.bic.mni.mcgill.ca, you
> > will get version 1.5.1 and also if you sourced from /mirror/mni-packages
> > between May 10th and this morning.
> >
> > As for why mincinfo version 1.5.1 is broken, ask Andrew.
> >
> > S
> >
> >
> >  On Tue, 15 May 2007, Alex ZIJDENBOS wrote:
> >
> > > Hallo all,
> > >
> > > I've been scratching my head on this one for a while now, and I'm
> > > still stuck. I have a MINC installation on a debian sarge machine
> > > which used to work fine and is suddenly broken:
> > >
> > > $ mincinfo -help
> > > mincinfo: /lib/tls/libc.so.6: version `GLIBC_2.4' not found (required by mincinfo)
> > >
> > > My (so far unconfirmed) suspicion is that this happened the last time
> > > I ran apt-get update/upgrade, which installed
> > >
> > >   libc6 2.3.2.ds1-22sarge6
> > >
> > > the previous version was either -sarge4 or -sarge5
> > >
> > > Anybody else run into this?
> > >
> > > Thanks,
> > >
> > > -- Alex
> > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> > ---
> > Sylvain Milot (sylvain at bic.mni.mcgill.ca)
> >               (bicadmin at bic.mni.mcgill.ca)
> > Brain Imaging Centre
> > Montreal Neurological Institute
> > 3801 University Street
> > Webster 2B, Room 208
> > Montreal, Qc., Canada, H3A 2B4
> > Phone  : (514) 398-4965, Fax: 398-8948
> > Mobile : (514) 712-1768
> > Office : 527 Av Des Pins O., Room 204
> >          Montreal, Qc., H2W 1S4
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From a.janke at gmail.com  Tue May 22 10:58:40 2007
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 23 May 2007 00:58:40 +1000
Subject: [MINC-users] ITK and MINC.
Message-ID: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>

Hi all,

For those who have an interest in ITK and MINC, have your say here.

   http://www.itk.org/Wiki/Proposals:Adding_MINC_File_Format

I have been asked to help finish of what as to be done to get it
included in the base ITK distribution, so now is the time to get your
requests/coments/offers of help in. I have left a space at the bottom
for those who wish to add things.


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From dfwang at cse.cuhk.edu.hk  Tue May 22 11:39:45 2007
From: dfwang at cse.cuhk.edu.hk (Defeng WANG)
Date: Tue, 22 May 2007 23:39:45 +0800
Subject: [MINC-users] ITK and MINC.
References: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
Message-ID: <010d01c79c87$6f455040$a459bd89@PC89164>

That's great!

----- Original Message ----- 
From: "Andrew Janke" <a.janke at gmail.com>
To: "geeks" <geeks at bic.mni.mcgill.ca>; "MINC users mailing list" 
<minc-users at bic.mni.mcgill.ca>; "minc-dev" 
<minc-development at bic.mni.mcgill.ca>
Sent: Tuesday, May 22, 2007 10:58 PM
Subject: [MINC-users] ITK and MINC.


> Hi all,
>
> For those who have an interest in ITK and MINC, have your say here.
>
>   http://www.itk.org/Wiki/Proposals:Adding_MINC_File_Format
>
> I have been asked to help finish of what as to be done to get it
> included in the base ITK distribution, so now is the time to get your
> requests/coments/offers of help in. I have left a space at the bottom
> for those who wish to add things.
>
>
> -- 
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users 


From vladimir.fonov at gmail.com  Tue May 22 11:45:24 2007
From: vladimir.fonov at gmail.com (Vladimir FONOV)
Date: Tue, 22 May 2007 11:45:24 -0400
Subject: [MINC-users] ITK and MINC.
In-Reply-To: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
References: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
Message-ID: <ea3878950705220845g5f3fd368oad6e85f02b640685@mail.gmail.com>

Hello,

On 5/22/07, Andrew Janke <a.janke at gmail.com> wrote:
> Hi all,
>
> For those who have an interest in ITK and MINC, have your say here.
>
>    http://www.itk.org/Wiki/Proposals:Adding_MINC_File_Format
>
> I have been asked to help finish of what as to be done to get it
> included in the base ITK distribution, so now is the time to get your
> requests/coments/offers of help in. I have left a space at the bottom
> for those who wish to add things.

Should we make it available as patch ?

-- 
Best regards,
 Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From sean at rogue-research.com  Thu May 24 13:43:00 2007
From: sean at rogue-research.com (Sean McBride)
Date: Thu, 24 May 2007 13:43:00 -0400
Subject: [MINC-users] [MINC-development] ITK and MINC.
In-Reply-To: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
References: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
Message-ID: <20070524174300.649746231@smtp1.sympatico.ca>

On 2007-05-23 00:58, Andrew Janke said:

>For those who have an interest in ITK and MINC, have your say here.
>
>   http://www.itk.org/Wiki/Proposals:Adding_MINC_File_Format
>
>I have been asked to help finish of what as to be done to get it
>included in the base ITK distribution, so now is the time to get your
>requests/coments/offers of help in. I have left a space at the bottom
>for those who wish to add things.

Andrew,

Not sure what I could/should say on the wiki, but I just wanted to say
that it would be great if MINC support was in the base ITK
distribution!  We would definitely be willing to help test any new
builds you have.  We are currently using Leila's stuff from the ITK
journal, it seems to work fine, though we have not stress-tested it.

Cheers,

-- 
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com 
Mac Software Developer              Montr?al, Qu?bec, Canada




From Michel.Audette at medizin.uni-leipzig.de  Thu May 24 14:41:33 2007
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Thu, 24 May 2007 20:41:33 +0200
Subject: [MINC-users] [MINC-development] ITK and MINC.
References: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
	<20070524174300.649746231@smtp1.sympatico.ca>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011453DD@MRZS152229.medizin.uni-leipzig.de>

Hello, 
 
My experience with Leila's stuff was that it could get the voxel scaling wrong. As far as I know, Vladimir Fonov, of Louis Collins' group, may have an ITK MINC reader that is more robust, but I have not yet tried it. 
 
Sean, please give my regards to Roch Comeau.
 
Cheers,

Michel

Michel Audette, Ph.D.  

Innovation Center Computer Assisted Surgery (ICCAS)  

Philipp-Rosenthal-Strasse 55 

Leipzig, Germany 

Phone: ++49 (0) 341 / 97 - 1 20 13 

Fax: ++49 (0) 341 / 97 - 1 20 09 

________________________________

From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Sean McBride
Sent: Thu 5/24/2007 7:43 PM
To: MINC development discussion & planning; Andrew Janke; geeks; MINC users mailing list
Subject: Re: [MINC-users] [MINC-development] ITK and MINC.



On 2007-05-23 00:58, Andrew Janke said:

>For those who have an interest in ITK and MINC, have your say here.
>
>   http://www.itk.org/Wiki/Proposals:Adding_MINC_File_Format
>
>I have been asked to help finish of what as to be done to get it
>included in the base ITK distribution, so now is the time to get your
>requests/coments/offers of help in. I have left a space at the bottom
>for those who wish to add things.

Andrew,

Not sure what I could/should say on the wiki, but I just wanted to say
that it would be great if MINC support was in the base ITK
distribution!  We would definitely be willing to help test any new
builds you have.  We are currently using Leila's stuff from the ITK
journal, it seems to work fine, though we have not stress-tested it.

Cheers,

--
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com
Mac Software Developer              Montr?al, Qu?bec, Canada



_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users



From vladimir.fonov at gmail.com  Thu May 24 14:50:56 2007
From: vladimir.fonov at gmail.com (Vladimir FONOV)
Date: Thu, 24 May 2007 14:50:56 -0400
Subject: [MINC-users] [MINC-development] ITK and MINC.
In-Reply-To: <160E3DD4FB702C4CB860C65186686E69011453DD@MRZS152229.medizin.uni-leipzig.de>
References: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
	<20070524174300.649746231@smtp1.sympatico.ca>
	<160E3DD4FB702C4CB860C65186686E69011453DD@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <ea3878950705241150w401b7cb0ib8e31a1b8af9149f@mail.gmail.com>

Hello,

On 5/24/07, Audette, Michel <Michel.Audette at medizin.uni-leipzig.de> wrote:
> Hello,
>
> My experience with Leila's stuff was that it could get the voxel scaling wrong. As far as I know, Vladimir Fonov, of Louis Collins' group, may have an ITK MINC reader that is more robust, but I have not yet tried it.

yes, I have a primitive interface based on the mincextract and
rawtominc . It is more limited than Leila'a stuff, but works with minc
1


-- 
Best regards,
 Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From rbrooks at cyberus.ca  Fri May 25 08:20:40 2007
From: rbrooks at cyberus.ca (Rupert Brooks)
Date: Fri, 25 May 2007 08:20:40 -0400
Subject: [MINC-users] ITK and MINC.
In-Reply-To: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
References: <d747ed50705220758y17fe3c11iaa276a185a870244@mail.gmail.com>
Message-ID: <a6cc33f0705250520h50f860a2re4d040e6036f17bb@mail.gmail.com>

Hi,

I think its an excellent idea   I've been using Leilas itkMINCReader
for quite a while now.  It works, but i can produce datasets that will
cause it to fail if i dont keep the axes ordering as zyx, all facing
in the +1 direction.  I'd be interested to help with the testing
process.

I think that minc1 reading is important.  Unless 2.0 is really out of
beta, and all the minc related tools - EMMA, register, etc are
upgraded to handle the 2.0 format, then i think there will be a lot of
people who want to keep their data in minc1.

Rupert

-- 
--------------------------------------------------------------
Rupert Brooks
McGill Centre for Intelligent Machines (www.cim.mcgill.ca)
Ph.D Student
http://www.cyberus.ca/~rbrooks

From alex at bic.mni.mcgill.ca  Mon May 28 15:13:25 2007
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Mon, 28 May 2007 15:13:25 -0400
Subject: [MINC-users] brain-view binary (and source packages).
In-Reply-To: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
References: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
Message-ID: <e758a6650705281213r10c5232aief4a72c53f4c0f37@mail.gmail.com>

Interesting typo, the missing 'l' in the deb link below - took me a
bit to figure out why I was looking at a very unusual page :-)

Say, two questions:

- pcre++ does not seem to exist for debian sarge stable (only in
unstable or testing, which would turn my sarge system upside down if I
try to install from there). After wrestling with it for some time I'm
still unclear how to get brain-view to go on debian sarge.

- the brain-view package on packages.bic is 0.6.2; but locally at the
bic a package barin-view-x86-bic 1.0 is installed. What's the
difference, and why?

Thanks,

-- A



On 5/10/07, Andrew Janke <a.janke at gmail.com> wrote:
> Finally I have this done,
>
> get it fresh from:
>
>    packages.bic.mni.mcgil.ca/deb
>
> or in source from
>
>    packages.bic.mni.mcgill.ca/tgz
>
> Note that this thing has a heap of dependencies that I have no
> included as pre-requisites in the package if only because I am sure
> there are a few versions of COIN and the likes out there.
>
> So, on my system (ubuntu feisty), I had to install these packages.
>
>    apt-get install libpcre3 libglut3 libxmu6 libxi6 libcoin40c2
> libqt3-mt libsoqt20
>
> once you have these and the packages line in your sources.list just type:
>
>    apt-get install brain-view
>
>
>
>
> ------
>
>
> Now if you want to build it from source (hey there are those out there
> who might like to).
>
> you will need to download these source packages from /tgz
>
>    arguments-0.2.1.tar.gz
>    bicInventor-0.3.1.tar.gz
>    oobicpl-0.4.3.tar.gz
>    brain-view-0.6.2.tar.gz
>
> and them make them in that order.  Of course you will also (if you are
> on a debian system have to install this lot:
>
>    apt-get install libpcre3-dev libglut3-dev libxmu-dev libxi-dev \
>       libcoin40-dev libqt3-mt-dev libsoqt-dev
>
> and you still wont be finished as then you will have to (if you are on
> ubuntu) go and get these:
>
>    libpcre++-dev_0.9.5-2_i386.deb
>    libpcre++0_0.9.5-2_i386.deb
>
> If you are a debian user, then just apt-get them.
>
> good luck...
>
> The usual Mac packages will follow in time, as usual there are a few
> quirks with them.  I know Jason has this working so it should not be
> that much of a problem.
>
> Now, who was it out there who had volunteered to write a wiki page for
> this if I made the package? :)
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From sylvain at bic.mni.mcgill.ca  Mon May 28 15:49:11 2007
From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT)
Date: Mon, 28 May 2007 15:49:11 -0400
Subject: [MINC-users] brain-view binary (and source packages).
In-Reply-To: <e758a6650705281213r10c5232aief4a72c53f4c0f37@mail.gmail.com>
References: <d747ed50705100901pb807625pd7cf234e5481c0af@mail.gmail.com>
	<e758a6650705281213r10c5232aief4a72c53f4c0f37@mail.gmail.com>
Message-ID: <Pine.SGI.4.58.0705281546000.20472574@yorick.bic.mni.mcgill.ca>


dpkg -s brain-view-x86-bic

S


On Mon, 28 May 2007, Alex Zijdenbos wrote:

> Interesting typo, the missing 'l' in the deb link below - took me a
> bit to figure out why I was looking at a very unusual page :-)
>
> Say, two questions:
>
> - pcre++ does not seem to exist for debian sarge stable (only in
> unstable or testing, which would turn my sarge system upside down if I
> try to install from there). After wrestling with it for some time I'm
> still unclear how to get brain-view to go on debian sarge.
>
> - the brain-view package on packages.bic is 0.6.2; but locally at the
> bic a package barin-view-x86-bic 1.0 is installed. What's the
> difference, and why?
>
> Thanks,
>
> -- A
>
>
>
> On 5/10/07, Andrew Janke <a.janke at gmail.com> wrote:
> > Finally I have this done,
> >
> > get it fresh from:
> >
> >    packages.bic.mni.mcgil.ca/deb
> >
> > or in source from
> >
> >    packages.bic.mni.mcgill.ca/tgz
> >
> > Note that this thing has a heap of dependencies that I have no
> > included as pre-requisites in the package if only because I am sure
> > there are a few versions of COIN and the likes out there.
> >
> > So, on my system (ubuntu feisty), I had to install these packages.
> >
> >    apt-get install libpcre3 libglut3 libxmu6 libxi6 libcoin40c2
> > libqt3-mt libsoqt20
> >
> > once you have these and the packages line in your sources.list just type:
> >
> >    apt-get install brain-view
> >
> >
> >
> >
> > ------
> >
> >
> > Now if you want to build it from source (hey there are those out there
> > who might like to).
> >
> > you will need to download these source packages from /tgz
> >
> >    arguments-0.2.1.tar.gz
> >    bicInventor-0.3.1.tar.gz
> >    oobicpl-0.4.3.tar.gz
> >    brain-view-0.6.2.tar.gz
> >
> > and them make them in that order.  Of course you will also (if you are
> > on a debian system have to install this lot:
> >
> >    apt-get install libpcre3-dev libglut3-dev libxmu-dev libxi-dev \
> >       libcoin40-dev libqt3-mt-dev libsoqt-dev
> >
> > and you still wont be finished as then you will have to (if you are on
> > ubuntu) go and get these:
> >
> >    libpcre++-dev_0.9.5-2_i386.deb
> >    libpcre++0_0.9.5-2_i386.deb
> >
> > If you are a debian user, then just apt-get them.
> >
> > good luck...
> >
> > The usual Mac packages will follow in time, as usual there are a few
> > quirks with them.  I know Jason has this working so it should not be
> > that much of a problem.
> >
> > Now, who was it out there who had volunteered to write a wiki page for
> > this if I made the package? :)
> >
> >
> > --
> > Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> > Canberra->Australia    +61 (402) 700 883
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (bicadmin at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4

From Michel.Audette at medizin.uni-leipzig.de  Tue May 29 06:20:46 2007
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Tue, 29 May 2007 12:20:46 +0200
Subject: [MINC-users] dicom3_to_minc failing on some Siemens data sets...
Message-ID: <160E3DD4FB702C4CB860C65186686E69015F1AF9@MRZS152229.medizin.uni-leipzig.de>

Hi everyone, 

I have stumbled on some Siemens data sets on which dicom3_to_minc seems to fail... 

I am seeing ERROR: Code SQ, length (some number that does not make sense)
Wrong number of bits allocated per image()

Using DicomDumper, I have reproduced the header below. DicomWorks is able to visualize the data. 

Can anyone suggest a means of debugging this and/or a simple workaround? Thanks for your help. 

Cheers, 

Michel

P.S.: DicomDumper cut-and-paste: 

(0002,0000) [Group Length] --> VR: UL, VL: 4
    Value: 204
(0002,0001) [File Meta Information Version] --> VR: OB, VL: 2
    Value: [string of bytes]
(0002,0002) [Media Storage SOP Class UID] --> VR: UI, VL: 26
    Value: 1.2.840.10008.5.1.4.1.1.2
(0002,0003) [Media Storage SOP Instance UID] --> VR: UI, VL: 46
    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
(0002,0010) [Transfer Syntax UID] --> VR: UI, VL: 20
    Value: 1.2.840.10008.1.2.1
(0002,0012) [Implementation Class UID] --> VR: UI, VL: 20
    Value: 1.2.276.0.19.1996.1
(0002,0013) [Implementation Version Name] --> VR: SH, VL: 14
    Value: VTServer 4.32
(0002,0016) [Source Application Entity Title] --> VR: AE, VL: 16
    Value: AN_CT38357
(0008,0000) [Group Length] --> VR: UL, VL: 4
    Value: 754
(0008,0005) [Specific Character Set] --> VR: CS, VL: 10
    Value: ISO_IR 100
(0008,0008) [Image Type] --> VR: CS, VL: 34
    Value: ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI
(0008,0016) [SOP Class UID] --> VR: UI, VL: 26
    Value: 1.2.840.10008.5.1.4.1.1.2
(0008,0018) [SOP Instance UID] --> VR: UI, VL: 46
    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
(0008,0020) [Study Date] --> VR: DA, VL: 8
    Value: 20070404
(0008,0021) [Series Date] --> VR: DA, VL: 8
    Value: 20070404
(0008,0022) [Acquisition Date] --> VR: DA, VL: 8
    Value: 20070404
(0008,0023) [Content Date] --> VR: DA, VL: 8
    Value: 20070404
(0008,0030) [Study Time] --> VR: TM, VL: 14
    Value: 161137.390000
(0008,0031) [Series Time] --> VR: TM, VL: 6
    Value: 161252
(0008,0032) [Acquisition Time] --> VR: TM, VL: 14
    Value: 161301.963478
(0008,0033) [Content Time] --> VR: TM, VL: 14
    Value: 161301.963478
(0008,0050) [Accession Number] --> VR: SH, VL: 0
    Value: 
(0008,0060) [Modality] --> VR: CS, VL: 2
    Value: CT
(0008,0070) [Manufacturer] --> VR: LO, VL: 8
    Value: SIEMENS
(0008,0080) [Institution Name] --> VR: LO, VL: 30
    Value: Rad.Nuk.med.Gemeischaftspraxis
(0008,0081) [Institution Address] --> VR: ST, VL: 50
    Value: Johannisplatz
Leipzig/2f0cd3/
Leipzig
Deutschland 
(0008,0090) [Referring Physician's Name] --> VR: PN, VL: 0
    Value: 
(0008,1010) [Station Name] --> VR: SH, VL: 8
    Value: CT38357
(0008,1030) [Study Description] --> VR: LO, VL: 20
    Value: Sch?del^09_Brainlab
(0008,103E) [Series Description] --> VR: LO, VL: 14
    Value: axial 2.0 H40s
(0008,1090) [Manufacturer's Model Name] --> VR: LO, VL: 8
    Value: Balance
(0008,1140) [Referenced Image Sequence] --> VR: SQ, VL: 4294967295
    Value: [sequence of elements]
	* Item 1
		(0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 26
		    Value: 1.2.840.10008.5.1.4.1.1.2
		(0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
		    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217900015152526
(0008,2112) [Source Image Sequence] --> VR: SQ, VL: 4294967295
    Value: [sequence of elements]
	* Item 1
		(0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 20
		    Value: 1.3.12.2.1107.5.9.1
		(0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
		    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217905113681033
(0009,0000) [Group Length] --> VR: UL, VL: 4
    Value: 28
(0009,0010) [Unknown Name] --> VR: LO, VL: 20
    Value: SIEMENS CT VA1 DUMMY
(0010,0000) [Group Length] --> VR: UL, VL: 4
    Value: 94
(0010,0010) [Patient's Name] --> VR: PN, VL: 18
    Value: K?hler^Wolfgang^^^
(0010,0020) [Patient Id] --> VR: LO, VL: 6
    Value: 69128
(0010,0030) [Patient's Birth Date] --> VR: DA, VL: 8
    Value: 19350307
(0010,0040) [Patient's Sex] --> VR: CS, VL: 2
    Value: M
(0010,1010) [Patient's Age] --> VR: AS, VL: 4
    Value: 072Y
(0010,1020) [Patient's Size] --> VR: DS, VL: 0
    Value: 
(0010,1030) [Patient's Weight] --> VR: DS, VL: 0
    Value: 
(0018,0000) [Group Length] --> VR: UL, VL: 4
    Value: 262
(0018,0015) [Body Part Examined] --> VR: CS, VL: 4
    Value: HEAD
(0018,0050) [Slice Thickness] --> VR: DS, VL: 2
    Value: 2
(0018,0060) [KVP] --> VR: DS, VL: 4
    Value: 130
(0018,1020) [Software Version(s)] --> VR: LO, VL: 6
    Value: VA47C
(0018,1030) [Protocol Name] --> VR: LO, VL: 12
    Value: 09_Brainlab
(0018,1100) [Reconstruction Diameter] --> VR: DS, VL: 4
    Value: 282
(0018,1110) [Distance Source to Detector] --> VR: DS, VL: 4
    Value: 940
(0018,1111) [Distance Source to Patient] --> VR: DS, VL: 4
    Value: 535
(0018,1120) [Gantry/Detector Tilt] --> VR: DS, VL: 2
    Value: 0
(0018,1130) [Table Height] --> VR: DS, VL: 4
    Value: 160
(0018,1140) [Rotation Direction] --> VR: CS, VL: 2
    Value: CW
(0018,1150) [Exposure Time] --> VR: IS, VL: 4
    Value: 1000
(0018,1151) [X-ray Tube Current] --> VR: IS, VL: 2
    Value: 90
(0018,1152) [Exposure] --> VR: IS, VL: 2
    Value: 90
(0018,1160) [Filter Type] --> VR: SH, VL: 2
    Value: 1
(0018,1170) [Generator Power] --> VR: IS, VL: 2
    Value: 11
(0018,1190) [Focal Spot(s)] --> VR: DS, VL: 4
    Value: 0.95
(0018,1200) [Date of Last Calibration] --> VR: DA, VL: 8
    Value: 20070404
(0018,1201) [Time of Last Calibration] --> VR: TM, VL: 14
    Value: 060159.000000
(0018,1210) [Convolution Kernel] --> VR: SH, VL: 4
    Value: H40s
(0018,5100) [Patient Position] --> VR: CS, VL: 4
    Value: HFS
(0019,0000) [Group Length] --> VR: UL, VL: 4
    Value: 38
(0019,0010) [Unknown Name] --> VR: LO, VL: 20
    Value: SIEMENS CT VA0  COAD
(0019,10B0) [Unknown Name] --> VR: DS, VL: 2
    Value: 2
(0020,0000) [Group Length] --> VR: UL, VL: 4
    Value: 284
(0020,000D) [Study Instance UID] --> VR: UI, VL: 46
    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217453428112303
(0020,000E) [Series Instance UID] --> VR: UI, VL: 46
    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217907287251360
(0020,0010) [Study Id] --> VR: SH, VL: 2
    Value: 2
(0020,0011) [Series Number] --> VR: IS, VL: 2
    Value: 2
(0020,0012) [Acquisition Number] --> VR: IS, VL: 2
    Value: 2
(0020,0013) [Instance Number] --> VR: IS, VL: 2
    Value: 1
(0020,0032) [Image Position (Patient)] --> VR: DS, VL: 26
    Value: -140.72461\-317.72461\-160
(0020,0037) [Image Orientation (Patient)] --> VR: DS, VL: 12
    Value: 1\0\0\0\1\0
(0020,0052) [Frame of Reference UID] --> VR: UI, VL: 46
    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217896016622697
(0020,1040) [Position Reference Indicator] --> VR: LO, VL: 0
    Value: 
(0020,1041) [Slice Location] --> VR: DS, VL: 4
    Value: -160
(0020,4000) [Image Comments] --> VR: LT, VL: 0
    Value: 
(0021,0000) [Group Length] --> VR: UL, VL: 4
    Value: 34
(0021,0010) [Unknown Name] --> VR: LO, VL: 12
    Value: SIEMENS MED
(0021,1011) [Unknown Name] --> VR: DS, VL: 6
    Value: 0\-17
(0028,0000) [Group Length] --> VR: UL, VL: 4
    Value: 198
(0028,0002) [Samples per Pixel] --> VR: US, VL: 2
    Value: 1
(0028,0004) [Photometric Interpretation] --> VR: CS, VL: 12
    Value: MONOCHROME2
(0028,0010) [Rows] --> VR: US, VL: 2
    Value: 512
(0028,0011) [Columns] --> VR: US, VL: 2
    Value: 512
(0028,0030) [Pixel Spacing] --> VR: DS, VL: 22
    Value: 0.55078125\0.55078125
(0028,0100) [Bits Allocated] --> VR: US, VL: 2
    Value: 16
(0028,0101) [Bits Stored] --> VR: US, VL: 2
    Value: 12
(0028,0102) [High Bit] --> VR: US, VL: 2
    Value: 11
(0028,0103) [Pixel Representation] --> VR: US, VL: 2
    Value: 0
(0028,1050) [Window Center] --> VR: DS, VL: 6
    Value: 40\700
(0028,1051) [Window Width] --> VR: DS, VL: 8
    Value: 200\3200
(0028,1052) [Rescale Intercept] --> VR: DS, VL: 6
    Value: -1024
(0028,1053) [Rescale Slope] --> VR: DS, VL: 2
    Value: 1
(0028,1055) [Window Center & Width Explanation] --> VR: LO, VL: 16
    Value: WINDOW1\WINDOW2
(0029,0000) [Group Length] --> VR: UL, VL: 4
    Value: 560
(0029,0010) [Unknown Name] --> VR: LO, VL: 18
    Value: SIEMENS CSA HEADER
(0029,0011) [Unknown Name] --> VR: LO, VL: 22
    Value: SIEMENS MEDCOM HEADER
(0029,1008) [Unknown Name] --> VR: CS, VL: 6
    Value: SOM 5
(0029,1009) [Unknown Name] --> VR: LO, VL: 12
    Value: VA10A 971201
(0029,1010) [Unknown Name] --> VR: OB, VL: 418
    Value: [string of bytes]
(0029,1131) [Unknown Name] --> VR: LO, VL: 12
    Value: 4.0.92170301
(0029,1134) [Unknown Name] --> VR: CS, VL: 12
    Value: DB TO DICOM
(0032,0000) [Group Length] --> VR: UL, VL: 4
    Value: 28
(0032,1060) [Requested Procedure Description] --> VR: LO, VL: 20
    Value: Sch?del 09_Brainlab
(0055,0000) [Group Length] --> VR: UL, VL: 4
    Value: 8542
(0055,0010) [Unknown Name] --> VR: LO, VL: 18
    Value: VEPRO VIF 3.0 DATA
(0055,1020) [Unknown Name] --> VR: OB, VL: 2048
    Value: [string of bytes]
(0055,1030) [Unknown Name] --> VR: OB, VL: 6412
    Value: [string of bytes]
(0055,1065) [Unknown Name] --> VR: OB, VL: 20
    Value: [string of bytes]
(0059,0000) [Group Length] --> VR: UL, VL: 4
    Value: 274
(0059,0010) [Unknown Name] --> VR: LO, VL: 24
    Value: VEPRO DICOM TRANSFER 1.0
(0059,1010) [Unknown Name] --> VR: SQ, VL: 4294967295
    Value: [sequence of elements]
	* Item 1
		(0059,0010) [Unknown Name] --> VR: LO, VL: 28
		    Value: VEPRO DICOM RECEIVE DATA 1.0
		(0059,1040) [Unknown Name] --> VR: DA, VL: 8
		    Value: 20070404
		(0059,1041) [Unknown Name] --> VR: TM, VL: 6
		    Value: 160913
		(0059,1042) [Unknown Name] --> VR: ST, VL: 10
		    Value: SIEMENS_CT
		(0059,1043) [Unknown Name] --> VR: ST, VL: 8
		    Value: VCONTROL
		(0059,1050) [Unknown Name] --> VR: ST, VL: 8
		    Value: vepro102
		(0059,1051) [Unknown Name] --> VR: ST, VL: 16
		    Value: VTSERVER        
		(0059,1060) [Unknown Name] --> VR: ST, VL: 12
		    Value: 10.10.29.53 
		(0059,1061) [Unknown Name] --> VR: ST, VL: 10
		    Value: AN_CT38357
		(0059,1070) [Unknown Name] --> VR: UI, VL: 20
		    Value: 1.2.840.10008.1.2.1
(7FE0,0000) [Group Length] --> VR: UL, VL: 4
    Value: 524300
(7FE0,0010) [Pixel Data] --> VR: OW, VL: 524288
    Value: [string of words]


Michel Audette, Ph.D.  
Innovation Center Computer Assisted Surgery (ICCAS)  
Philipp-Rosenthal-Strasse 55 
Leipzig, Germany 
Phone: ++49 (0) 341 / 97 - 1 20 13 
Fax: ++49 (0) 341 / 97 - 1 20 09 
 


From jharlap at bic.mni.mcgill.ca  Tue May 29 07:45:36 2007
From: jharlap at bic.mni.mcgill.ca (Jon Harlap)
Date: Tue, 29 May 2007 07:45:36 -0400
Subject: [MINC-users] dicom3_to_minc failing on some Siemens data sets...
In-Reply-To: <160E3DD4FB702C4CB860C65186686E69015F1AF9@MRZS152229.medizin.uni-leipzig.de>
References: <160E3DD4FB702C4CB860C65186686E69015F1AF9@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <465C1260.5080500@bic.mni.mcgill.ca>

Hi Michel,

This is because DICOMperl (the library upon which dicom3_to_minc is 
based) does not support DICOM sequences with undefined length.  I'd 
suggest that you either:

a) use dcm2mnc (included with MINC) to convert your data instead of 
dicom3_to_minc.

b) or try to use dcmtk (dcmconv or dcmodify) to fix the sequence's 
length info to be defined.

Cheers,
J


Audette, Michel wrote:
> Hi everyone, 
> 
> I have stumbled on some Siemens data sets on which dicom3_to_minc seems to fail... 
> 
> I am seeing ERROR: Code SQ, length (some number that does not make sense)
> Wrong number of bits allocated per image()
> 
> Using DicomDumper, I have reproduced the header below. DicomWorks is able to visualize the data. 
> 
> Can anyone suggest a means of debugging this and/or a simple workaround? Thanks for your help. 
> 
> Cheers, 
> 
> Michel
> 
> P.S.: DicomDumper cut-and-paste: 
> 
> (0002,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 204
> (0002,0001) [File Meta Information Version] --> VR: OB, VL: 2
>     Value: [string of bytes]
> (0002,0002) [Media Storage SOP Class UID] --> VR: UI, VL: 26
>     Value: 1.2.840.10008.5.1.4.1.1.2
> (0002,0003) [Media Storage SOP Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
> (0002,0010) [Transfer Syntax UID] --> VR: UI, VL: 20
>     Value: 1.2.840.10008.1.2.1
> (0002,0012) [Implementation Class UID] --> VR: UI, VL: 20
>     Value: 1.2.276.0.19.1996.1
> (0002,0013) [Implementation Version Name] --> VR: SH, VL: 14
>     Value: VTServer 4.32
> (0002,0016) [Source Application Entity Title] --> VR: AE, VL: 16
>     Value: AN_CT38357
> (0008,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 754
> (0008,0005) [Specific Character Set] --> VR: CS, VL: 10
>     Value: ISO_IR 100
> (0008,0008) [Image Type] --> VR: CS, VL: 34
>     Value: ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI
> (0008,0016) [SOP Class UID] --> VR: UI, VL: 26
>     Value: 1.2.840.10008.5.1.4.1.1.2
> (0008,0018) [SOP Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
> (0008,0020) [Study Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0021) [Series Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0022) [Acquisition Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0023) [Content Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0030) [Study Time] --> VR: TM, VL: 14
>     Value: 161137.390000
> (0008,0031) [Series Time] --> VR: TM, VL: 6
>     Value: 161252
> (0008,0032) [Acquisition Time] --> VR: TM, VL: 14
>     Value: 161301.963478
> (0008,0033) [Content Time] --> VR: TM, VL: 14
>     Value: 161301.963478
> (0008,0050) [Accession Number] --> VR: SH, VL: 0
>     Value: 
> (0008,0060) [Modality] --> VR: CS, VL: 2
>     Value: CT
> (0008,0070) [Manufacturer] --> VR: LO, VL: 8
>     Value: SIEMENS
> (0008,0080) [Institution Name] --> VR: LO, VL: 30
>     Value: Rad.Nuk.med.Gemeischaftspraxis
> (0008,0081) [Institution Address] --> VR: ST, VL: 50
>     Value: Johannisplatz
> Leipzig/2f0cd3/
> Leipzig
> Deutschland 
> (0008,0090) [Referring Physician's Name] --> VR: PN, VL: 0
>     Value: 
> (0008,1010) [Station Name] --> VR: SH, VL: 8
>     Value: CT38357
> (0008,1030) [Study Description] --> VR: LO, VL: 20
>     Value: Sch?del^09_Brainlab
> (0008,103E) [Series Description] --> VR: LO, VL: 14
>     Value: axial 2.0 H40s
> (0008,1090) [Manufacturer's Model Name] --> VR: LO, VL: 8
>     Value: Balance
> (0008,1140) [Referenced Image Sequence] --> VR: SQ, VL: 4294967295
>     Value: [sequence of elements]
> 	* Item 1
> 		(0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 26
> 		    Value: 1.2.840.10008.5.1.4.1.1.2
> 		(0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
> 		    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217900015152526
> (0008,2112) [Source Image Sequence] --> VR: SQ, VL: 4294967295
>     Value: [sequence of elements]
> 	* Item 1
> 		(0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 20
> 		    Value: 1.3.12.2.1107.5.9.1
> 		(0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
> 		    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217905113681033
> (0009,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 28
> (0009,0010) [Unknown Name] --> VR: LO, VL: 20
>     Value: SIEMENS CT VA1 DUMMY
> (0010,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 94
> (0010,0010) [Patient's Name] --> VR: PN, VL: 18
>     Value: K?hler^Wolfgang^^^
> (0010,0020) [Patient Id] --> VR: LO, VL: 6
>     Value: 69128
> (0010,0030) [Patient's Birth Date] --> VR: DA, VL: 8
>     Value: 19350307
> (0010,0040) [Patient's Sex] --> VR: CS, VL: 2
>     Value: M
> (0010,1010) [Patient's Age] --> VR: AS, VL: 4
>     Value: 072Y
> (0010,1020) [Patient's Size] --> VR: DS, VL: 0
>     Value: 
> (0010,1030) [Patient's Weight] --> VR: DS, VL: 0
>     Value: 
> (0018,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 262
> (0018,0015) [Body Part Examined] --> VR: CS, VL: 4
>     Value: HEAD
> (0018,0050) [Slice Thickness] --> VR: DS, VL: 2
>     Value: 2
> (0018,0060) [KVP] --> VR: DS, VL: 4
>     Value: 130
> (0018,1020) [Software Version(s)] --> VR: LO, VL: 6
>     Value: VA47C
> (0018,1030) [Protocol Name] --> VR: LO, VL: 12
>     Value: 09_Brainlab
> (0018,1100) [Reconstruction Diameter] --> VR: DS, VL: 4
>     Value: 282
> (0018,1110) [Distance Source to Detector] --> VR: DS, VL: 4
>     Value: 940
> (0018,1111) [Distance Source to Patient] --> VR: DS, VL: 4
>     Value: 535
> (0018,1120) [Gantry/Detector Tilt] --> VR: DS, VL: 2
>     Value: 0
> (0018,1130) [Table Height] --> VR: DS, VL: 4
>     Value: 160
> (0018,1140) [Rotation Direction] --> VR: CS, VL: 2
>     Value: CW
> (0018,1150) [Exposure Time] --> VR: IS, VL: 4
>     Value: 1000
> (0018,1151) [X-ray Tube Current] --> VR: IS, VL: 2
>     Value: 90
> (0018,1152) [Exposure] --> VR: IS, VL: 2
>     Value: 90
> (0018,1160) [Filter Type] --> VR: SH, VL: 2
>     Value: 1
> (0018,1170) [Generator Power] --> VR: IS, VL: 2
>     Value: 11
> (0018,1190) [Focal Spot(s)] --> VR: DS, VL: 4
>     Value: 0.95
> (0018,1200) [Date of Last Calibration] --> VR: DA, VL: 8
>     Value: 20070404
> (0018,1201) [Time of Last Calibration] --> VR: TM, VL: 14
>     Value: 060159.000000
> (0018,1210) [Convolution Kernel] --> VR: SH, VL: 4
>     Value: H40s
> (0018,5100) [Patient Position] --> VR: CS, VL: 4
>     Value: HFS
> (0019,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 38
> (0019,0010) [Unknown Name] --> VR: LO, VL: 20
>     Value: SIEMENS CT VA0  COAD
> (0019,10B0) [Unknown Name] --> VR: DS, VL: 2
>     Value: 2
> (0020,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 284
> (0020,000D) [Study Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217453428112303
> (0020,000E) [Series Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217907287251360
> (0020,0010) [Study Id] --> VR: SH, VL: 2
>     Value: 2
> (0020,0011) [Series Number] --> VR: IS, VL: 2
>     Value: 2
> (0020,0012) [Acquisition Number] --> VR: IS, VL: 2
>     Value: 2
> (0020,0013) [Instance Number] --> VR: IS, VL: 2
>     Value: 1
> (0020,0032) [Image Position (Patient)] --> VR: DS, VL: 26
>     Value: -140.72461\-317.72461\-160
> (0020,0037) [Image Orientation (Patient)] --> VR: DS, VL: 12
>     Value: 1\0\0\0\1\0
> (0020,0052) [Frame of Reference UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217896016622697
> (0020,1040) [Position Reference Indicator] --> VR: LO, VL: 0
>     Value: 
> (0020,1041) [Slice Location] --> VR: DS, VL: 4
>     Value: -160
> (0020,4000) [Image Comments] --> VR: LT, VL: 0
>     Value: 
> (0021,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 34
> (0021,0010) [Unknown Name] --> VR: LO, VL: 12
>     Value: SIEMENS MED
> (0021,1011) [Unknown Name] --> VR: DS, VL: 6
>     Value: 0\-17
> (0028,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 198
> (0028,0002) [Samples per Pixel] --> VR: US, VL: 2
>     Value: 1
> (0028,0004) [Photometric Interpretation] --> VR: CS, VL: 12
>     Value: MONOCHROME2
> (0028,0010) [Rows] --> VR: US, VL: 2
>     Value: 512
> (0028,0011) [Columns] --> VR: US, VL: 2
>     Value: 512
> (0028,0030) [Pixel Spacing] --> VR: DS, VL: 22
>     Value: 0.55078125\0.55078125
> (0028,0100) [Bits Allocated] --> VR: US, VL: 2
>     Value: 16
> (0028,0101) [Bits Stored] --> VR: US, VL: 2
>     Value: 12
> (0028,0102) [High Bit] --> VR: US, VL: 2
>     Value: 11
> (0028,0103) [Pixel Representation] --> VR: US, VL: 2
>     Value: 0
> (0028,1050) [Window Center] --> VR: DS, VL: 6
>     Value: 40\700
> (0028,1051) [Window Width] --> VR: DS, VL: 8
>     Value: 200\3200
> (0028,1052) [Rescale Intercept] --> VR: DS, VL: 6
>     Value: -1024
> (0028,1053) [Rescale Slope] --> VR: DS, VL: 2
>     Value: 1
> (0028,1055) [Window Center & Width Explanation] --> VR: LO, VL: 16
>     Value: WINDOW1\WINDOW2
> (0029,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 560
> (0029,0010) [Unknown Name] --> VR: LO, VL: 18
>     Value: SIEMENS CSA HEADER
> (0029,0011) [Unknown Name] --> VR: LO, VL: 22
>     Value: SIEMENS MEDCOM HEADER
> (0029,1008) [Unknown Name] --> VR: CS, VL: 6
>     Value: SOM 5
> (0029,1009) [Unknown Name] --> VR: LO, VL: 12
>     Value: VA10A 971201
> (0029,1010) [Unknown Name] --> VR: OB, VL: 418
>     Value: [string of bytes]
> (0029,1131) [Unknown Name] --> VR: LO, VL: 12
>     Value: 4.0.92170301
> (0029,1134) [Unknown Name] --> VR: CS, VL: 12
>     Value: DB TO DICOM
> (0032,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 28
> (0032,1060) [Requested Procedure Description] --> VR: LO, VL: 20
>     Value: Sch?del 09_Brainlab
> (0055,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 8542
> (0055,0010) [Unknown Name] --> VR: LO, VL: 18
>     Value: VEPRO VIF 3.0 DATA
> (0055,1020) [Unknown Name] --> VR: OB, VL: 2048
>     Value: [string of bytes]
> (0055,1030) [Unknown Name] --> VR: OB, VL: 6412
>     Value: [string of bytes]
> (0055,1065) [Unknown Name] --> VR: OB, VL: 20
>     Value: [string of bytes]
> (0059,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 274
> (0059,0010) [Unknown Name] --> VR: LO, VL: 24
>     Value: VEPRO DICOM TRANSFER 1.0
> (0059,1010) [Unknown Name] --> VR: SQ, VL: 4294967295
>     Value: [sequence of elements]
> 	* Item 1
> 		(0059,0010) [Unknown Name] --> VR: LO, VL: 28
> 		    Value: VEPRO DICOM RECEIVE DATA 1.0
> 		(0059,1040) [Unknown Name] --> VR: DA, VL: 8
> 		    Value: 20070404
> 		(0059,1041) [Unknown Name] --> VR: TM, VL: 6
> 		    Value: 160913
> 		(0059,1042) [Unknown Name] --> VR: ST, VL: 10
> 		    Value: SIEMENS_CT
> 		(0059,1043) [Unknown Name] --> VR: ST, VL: 8
> 		    Value: VCONTROL
> 		(0059,1050) [Unknown Name] --> VR: ST, VL: 8
> 		    Value: vepro102
> 		(0059,1051) [Unknown Name] --> VR: ST, VL: 16
> 		    Value: VTSERVER        
> 		(0059,1060) [Unknown Name] --> VR: ST, VL: 12
> 		    Value: 10.10.29.53 
> 		(0059,1061) [Unknown Name] --> VR: ST, VL: 10
> 		    Value: AN_CT38357
> 		(0059,1070) [Unknown Name] --> VR: UI, VL: 20
> 		    Value: 1.2.840.10008.1.2.1
> (7FE0,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 524300
> (7FE0,0010) [Pixel Data] --> VR: OW, VL: 524288
>     Value: [string of words]
> 
> 
> Michel Audette, Ph.D.  
> Innovation Center Computer Assisted Surgery (ICCAS)  
> Philipp-Rosenthal-Strasse 55 
> Leipzig, Germany 
> Phone: ++49 (0) 341 / 97 - 1 20 13 
> Fax: ++49 (0) 341 / 97 - 1 20 09 
>  
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From acveilleux at mrs.mni.mcgill.ca  Tue May 29 08:04:10 2007
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Tue, 29 May 2007 08:04:10 -0400
Subject: [MINC-users] dicom3_to_minc failing on some Siemens data sets...
In-Reply-To: <160E3DD4FB702C4CB860C65186686E69015F1AF9@MRZS152229.medizin.uni-leipzig.de>;
	from Michel.Audette@medizin.uni-leipzig.de on Tue, May 29, 2007 at
	12:20:46PM +0200
References: <160E3DD4FB702C4CB860C65186686E69015F1AF9@MRZS152229.medizin.uni-leipzig.de>
Message-ID: <20070529080410.A19057@mrs.mni.mcgill.ca>

	The ridiculous length is actually the value "-1" being read as
unsigned. If the image is not compressed, Peter Neelin's dicom_to_minc
ought to work on it.

Alex

On Tue, May 29, 2007 at 12:20:46PM +0200, Audette, Michel wrote:
> Date: Tue, 29 May 2007 12:20:46 +0200
> From: "Audette, Michel" <Michel.Audette at medizin.uni-leipzig.de>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] dicom3_to_minc failing on some Siemens data sets...
> 
> Hi everyone, 
> 
> I have stumbled on some Siemens data sets on which dicom3_to_minc seems to fail... 
> 
> I am seeing ERROR: Code SQ, length (some number that does not make sense)
> Wrong number of bits allocated per image()
> 
> Using DicomDumper, I have reproduced the header below. DicomWorks is able to visualize the data. 
> 
> Can anyone suggest a means of debugging this and/or a simple workaround? Thanks for your help. 
> 
> Cheers, 
> 
> Michel

From Michel.Audette at medizin.uni-leipzig.de  Tue May 29 09:16:31 2007
From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel)
Date: Tue, 29 May 2007 15:16:31 +0200
Subject: [MINC-users] dicom3_to_minc failing on some Siemens data sets...
References: <160E3DD4FB702C4CB860C65186686E69015F1AF9@MRZS152229.medizin.uni-leipzig.de>
	<465C1260.5080500@bic.mni.mcgill.ca>
Message-ID: <160E3DD4FB702C4CB860C65186686E69011453E8@MRZS152229.medizin.uni-leipzig.de>

Dear Jonathan and Alex,

thanks for the kind reply. Jonathan's suggestion did the trick. I try them both, dicom3_to_minc and dcm2mnc, in succession, in the future. 

Cheers,

Michel


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Jon Harlap
Sent: Tue 5/29/2007 1:45 PM
To: MINC users mailing list
Subject: Re: [MINC-users] dicom3_to_minc failing on some Siemens data sets...
 
Hi Michel,

This is because DICOMperl (the library upon which dicom3_to_minc is 
based) does not support DICOM sequences with undefined length.  I'd 
suggest that you either:

a) use dcm2mnc (included with MINC) to convert your data instead of 
dicom3_to_minc.

b) or try to use dcmtk (dcmconv or dcmodify) to fix the sequence's 
length info to be defined.

Cheers,
J


Audette, Michel wrote:
> Hi everyone, 
> 
> I have stumbled on some Siemens data sets on which dicom3_to_minc seems to fail... 
> 
> I am seeing ERROR: Code SQ, length (some number that does not make sense)
> Wrong number of bits allocated per image()
> 
> Using DicomDumper, I have reproduced the header below. DicomWorks is able to visualize the data. 
> 
> Can anyone suggest a means of debugging this and/or a simple workaround? Thanks for your help. 
> 
> Cheers, 
> 
> Michel
> 
> P.S.: DicomDumper cut-and-paste: 
> 
> (0002,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 204
> (0002,0001) [File Meta Information Version] --> VR: OB, VL: 2
>     Value: [string of bytes]
> (0002,0002) [Media Storage SOP Class UID] --> VR: UI, VL: 26
>     Value: 1.2.840.10008.5.1.4.1.1.2
> (0002,0003) [Media Storage SOP Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
> (0002,0010) [Transfer Syntax UID] --> VR: UI, VL: 20
>     Value: 1.2.840.10008.1.2.1
> (0002,0012) [Implementation Class UID] --> VR: UI, VL: 20
>     Value: 1.2.276.0.19.1996.1
> (0002,0013) [Implementation Version Name] --> VR: SH, VL: 14
>     Value: VTServer 4.32
> (0002,0016) [Source Application Entity Title] --> VR: AE, VL: 16
>     Value: AN_CT38357
> (0008,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 754
> (0008,0005) [Specific Character Set] --> VR: CS, VL: 10
>     Value: ISO_IR 100
> (0008,0008) [Image Type] --> VR: CS, VL: 34
>     Value: ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI
> (0008,0016) [SOP Class UID] --> VR: UI, VL: 26
>     Value: 1.2.840.10008.5.1.4.1.1.2
> (0008,0018) [SOP Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217910524932886
> (0008,0020) [Study Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0021) [Series Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0022) [Acquisition Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0023) [Content Date] --> VR: DA, VL: 8
>     Value: 20070404
> (0008,0030) [Study Time] --> VR: TM, VL: 14
>     Value: 161137.390000
> (0008,0031) [Series Time] --> VR: TM, VL: 6
>     Value: 161252
> (0008,0032) [Acquisition Time] --> VR: TM, VL: 14
>     Value: 161301.963478
> (0008,0033) [Content Time] --> VR: TM, VL: 14
>     Value: 161301.963478
> (0008,0050) [Accession Number] --> VR: SH, VL: 0
>     Value: 
> (0008,0060) [Modality] --> VR: CS, VL: 2
>     Value: CT
> (0008,0070) [Manufacturer] --> VR: LO, VL: 8
>     Value: SIEMENS
> (0008,0080) [Institution Name] --> VR: LO, VL: 30
>     Value: Rad.Nuk.med.Gemeischaftspraxis
> (0008,0081) [Institution Address] --> VR: ST, VL: 50
>     Value: Johannisplatz
> Leipzig/2f0cd3/
> Leipzig
> Deutschland 
> (0008,0090) [Referring Physician's Name] --> VR: PN, VL: 0
>     Value: 
> (0008,1010) [Station Name] --> VR: SH, VL: 8
>     Value: CT38357
> (0008,1030) [Study Description] --> VR: LO, VL: 20
>     Value: Sch?del^09_Brainlab
> (0008,103E) [Series Description] --> VR: LO, VL: 14
>     Value: axial 2.0 H40s
> (0008,1090) [Manufacturer's Model Name] --> VR: LO, VL: 8
>     Value: Balance
> (0008,1140) [Referenced Image Sequence] --> VR: SQ, VL: 4294967295
>     Value: [sequence of elements]
> 	* Item 1
> 		(0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 26
> 		    Value: 1.2.840.10008.5.1.4.1.1.2
> 		(0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
> 		    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217900015152526
> (0008,2112) [Source Image Sequence] --> VR: SQ, VL: 4294967295
>     Value: [sequence of elements]
> 	* Item 1
> 		(0008,1150) [Referenced SOP Class UID] --> VR: UI, VL: 20
> 		    Value: 1.3.12.2.1107.5.9.1
> 		(0008,1155) [Referenced SOP Instance UID] --> VR: UI, VL: 46
> 		    Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217905113681033
> (0009,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 28
> (0009,0010) [Unknown Name] --> VR: LO, VL: 20
>     Value: SIEMENS CT VA1 DUMMY
> (0010,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 94
> (0010,0010) [Patient's Name] --> VR: PN, VL: 18
>     Value: K?hler^Wolfgang^^^
> (0010,0020) [Patient Id] --> VR: LO, VL: 6
>     Value: 69128
> (0010,0030) [Patient's Birth Date] --> VR: DA, VL: 8
>     Value: 19350307
> (0010,0040) [Patient's Sex] --> VR: CS, VL: 2
>     Value: M
> (0010,1010) [Patient's Age] --> VR: AS, VL: 4
>     Value: 072Y
> (0010,1020) [Patient's Size] --> VR: DS, VL: 0
>     Value: 
> (0010,1030) [Patient's Weight] --> VR: DS, VL: 0
>     Value: 
> (0018,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 262
> (0018,0015) [Body Part Examined] --> VR: CS, VL: 4
>     Value: HEAD
> (0018,0050) [Slice Thickness] --> VR: DS, VL: 2
>     Value: 2
> (0018,0060) [KVP] --> VR: DS, VL: 4
>     Value: 130
> (0018,1020) [Software Version(s)] --> VR: LO, VL: 6
>     Value: VA47C
> (0018,1030) [Protocol Name] --> VR: LO, VL: 12
>     Value: 09_Brainlab
> (0018,1100) [Reconstruction Diameter] --> VR: DS, VL: 4
>     Value: 282
> (0018,1110) [Distance Source to Detector] --> VR: DS, VL: 4
>     Value: 940
> (0018,1111) [Distance Source to Patient] --> VR: DS, VL: 4
>     Value: 535
> (0018,1120) [Gantry/Detector Tilt] --> VR: DS, VL: 2
>     Value: 0
> (0018,1130) [Table Height] --> VR: DS, VL: 4
>     Value: 160
> (0018,1140) [Rotation Direction] --> VR: CS, VL: 2
>     Value: CW
> (0018,1150) [Exposure Time] --> VR: IS, VL: 4
>     Value: 1000
> (0018,1151) [X-ray Tube Current] --> VR: IS, VL: 2
>     Value: 90
> (0018,1152) [Exposure] --> VR: IS, VL: 2
>     Value: 90
> (0018,1160) [Filter Type] --> VR: SH, VL: 2
>     Value: 1
> (0018,1170) [Generator Power] --> VR: IS, VL: 2
>     Value: 11
> (0018,1190) [Focal Spot(s)] --> VR: DS, VL: 4
>     Value: 0.95
> (0018,1200) [Date of Last Calibration] --> VR: DA, VL: 8
>     Value: 20070404
> (0018,1201) [Time of Last Calibration] --> VR: TM, VL: 14
>     Value: 060159.000000
> (0018,1210) [Convolution Kernel] --> VR: SH, VL: 4
>     Value: H40s
> (0018,5100) [Patient Position] --> VR: CS, VL: 4
>     Value: HFS
> (0019,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 38
> (0019,0010) [Unknown Name] --> VR: LO, VL: 20
>     Value: SIEMENS CT VA0  COAD
> (0019,10B0) [Unknown Name] --> VR: DS, VL: 2
>     Value: 2
> (0020,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 284
> (0020,000D) [Study Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217453428112303
> (0020,000E) [Series Instance UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217907287251360
> (0020,0010) [Study Id] --> VR: SH, VL: 2
>     Value: 2
> (0020,0011) [Series Number] --> VR: IS, VL: 2
>     Value: 2
> (0020,0012) [Acquisition Number] --> VR: IS, VL: 2
>     Value: 2
> (0020,0013) [Instance Number] --> VR: IS, VL: 2
>     Value: 1
> (0020,0032) [Image Position (Patient)] --> VR: DS, VL: 26
>     Value: -140.72461\-317.72461\-160
> (0020,0037) [Image Orientation (Patient)] --> VR: DS, VL: 12
>     Value: 1\0\0\0\1\0
> (0020,0052) [Frame of Reference UID] --> VR: UI, VL: 46
>     Value: 1.3.12.2.1107.5.1.4.38357.4.0.9217896016622697
> (0020,1040) [Position Reference Indicator] --> VR: LO, VL: 0
>     Value: 
> (0020,1041) [Slice Location] --> VR: DS, VL: 4
>     Value: -160
> (0020,4000) [Image Comments] --> VR: LT, VL: 0
>     Value: 
> (0021,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 34
> (0021,0010) [Unknown Name] --> VR: LO, VL: 12
>     Value: SIEMENS MED
> (0021,1011) [Unknown Name] --> VR: DS, VL: 6
>     Value: 0\-17
> (0028,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 198
> (0028,0002) [Samples per Pixel] --> VR: US, VL: 2
>     Value: 1
> (0028,0004) [Photometric Interpretation] --> VR: CS, VL: 12
>     Value: MONOCHROME2
> (0028,0010) [Rows] --> VR: US, VL: 2
>     Value: 512
> (0028,0011) [Columns] --> VR: US, VL: 2
>     Value: 512
> (0028,0030) [Pixel Spacing] --> VR: DS, VL: 22
>     Value: 0.55078125\0.55078125
> (0028,0100) [Bits Allocated] --> VR: US, VL: 2
>     Value: 16
> (0028,0101) [Bits Stored] --> VR: US, VL: 2
>     Value: 12
> (0028,0102) [High Bit] --> VR: US, VL: 2
>     Value: 11
> (0028,0103) [Pixel Representation] --> VR: US, VL: 2
>     Value: 0
> (0028,1050) [Window Center] --> VR: DS, VL: 6
>     Value: 40\700
> (0028,1051) [Window Width] --> VR: DS, VL: 8
>     Value: 200\3200
> (0028,1052) [Rescale Intercept] --> VR: DS, VL: 6
>     Value: -1024
> (0028,1053) [Rescale Slope] --> VR: DS, VL: 2
>     Value: 1
> (0028,1055) [Window Center & Width Explanation] --> VR: LO, VL: 16
>     Value: WINDOW1\WINDOW2
> (0029,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 560
> (0029,0010) [Unknown Name] --> VR: LO, VL: 18
>     Value: SIEMENS CSA HEADER
> (0029,0011) [Unknown Name] --> VR: LO, VL: 22
>     Value: SIEMENS MEDCOM HEADER
> (0029,1008) [Unknown Name] --> VR: CS, VL: 6
>     Value: SOM 5
> (0029,1009) [Unknown Name] --> VR: LO, VL: 12
>     Value: VA10A 971201
> (0029,1010) [Unknown Name] --> VR: OB, VL: 418
>     Value: [string of bytes]
> (0029,1131) [Unknown Name] --> VR: LO, VL: 12
>     Value: 4.0.92170301
> (0029,1134) [Unknown Name] --> VR: CS, VL: 12
>     Value: DB TO DICOM
> (0032,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 28
> (0032,1060) [Requested Procedure Description] --> VR: LO, VL: 20
>     Value: Sch?del 09_Brainlab
> (0055,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 8542
> (0055,0010) [Unknown Name] --> VR: LO, VL: 18
>     Value: VEPRO VIF 3.0 DATA
> (0055,1020) [Unknown Name] --> VR: OB, VL: 2048
>     Value: [string of bytes]
> (0055,1030) [Unknown Name] --> VR: OB, VL: 6412
>     Value: [string of bytes]
> (0055,1065) [Unknown Name] --> VR: OB, VL: 20
>     Value: [string of bytes]
> (0059,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 274
> (0059,0010) [Unknown Name] --> VR: LO, VL: 24
>     Value: VEPRO DICOM TRANSFER 1.0
> (0059,1010) [Unknown Name] --> VR: SQ, VL: 4294967295
>     Value: [sequence of elements]
> 	* Item 1
> 		(0059,0010) [Unknown Name] --> VR: LO, VL: 28
> 		    Value: VEPRO DICOM RECEIVE DATA 1.0
> 		(0059,1040) [Unknown Name] --> VR: DA, VL: 8
> 		    Value: 20070404
> 		(0059,1041) [Unknown Name] --> VR: TM, VL: 6
> 		    Value: 160913
> 		(0059,1042) [Unknown Name] --> VR: ST, VL: 10
> 		    Value: SIEMENS_CT
> 		(0059,1043) [Unknown Name] --> VR: ST, VL: 8
> 		    Value: VCONTROL
> 		(0059,1050) [Unknown Name] --> VR: ST, VL: 8
> 		    Value: vepro102
> 		(0059,1051) [Unknown Name] --> VR: ST, VL: 16
> 		    Value: VTSERVER        
> 		(0059,1060) [Unknown Name] --> VR: ST, VL: 12
> 		    Value: 10.10.29.53 
> 		(0059,1061) [Unknown Name] --> VR: ST, VL: 10
> 		    Value: AN_CT38357
> 		(0059,1070) [Unknown Name] --> VR: UI, VL: 20
> 		    Value: 1.2.840.10008.1.2.1
> (7FE0,0000) [Group Length] --> VR: UL, VL: 4
>     Value: 524300
> (7FE0,0010) [Pixel Data] --> VR: OW, VL: 524288
>     Value: [string of words]
> 
> 
> Michel Audette, Ph.D.  
> Innovation Center Computer Assisted Surgery (ICCAS)  
> Philipp-Rosenthal-Strasse 55 
> Leipzig, Germany 
> Phone: ++49 (0) 341 / 97 - 1 20 13 
> Fax: ++49 (0) 341 / 97 - 1 20 09 
>  
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users