Re: [Teem-users] gradient from command line?

[Carlos Scheidegger <cscheid@sc...>]

you're probably looking for vprobe..

-carlos

> How do I casually take the gradient of a scalar field from the command
> line? I seem to recall that there is an example of this on the web
> page, but I couldn't track it down.
>
> -Thanks
> Abe
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
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> _______________________________________________
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[Teem-users] gradient from command line?

[Abe Stephens <abe@sc...>]

How do I casually take the gradient of a scalar field from the command  
line? I seem to recall that there is an example of this on the web  
page, but I couldn't track it down.

-Thanks
Abe

[Teem-users] B-matrix and B-values

[Daniel Ennis <daniel.ennis@gm...>]

Hi - I've got a rather screwy DTMRI dataset that I'm trying to recon with
tend estim.  I have been provided with the image data and also the diffusion
gradient encoding information that is contained below.  I'm a bit confused
as to how tend should use this info to obtain the b-matrix and the nominal
b-value.

Right now I am simply doing:

tend bmat -i $DNAME -o $BNAME

in order to create the b-matrix and then I'm using an nominal b-value of
1000 to which the gradients (below) grossly correspond. $DNAME is a text
file with the gradient directions as written below.

I guess the real question is how do we properly handle non-constant
b-values?  The gradients below have b-values in the range of ~110 to ~1770
and there is no b-value=0 dataset.  There is a comment in tend bmat about
not needing to normalize the gradient vector directions, but clearly the
b-value we pass to tend estim must stand in relation to gradients we used.
Which b-value should I be using?

In the end, to estimate the tensors I'm using the following:

tend bmat -i $DNAME -o $BNAME

The results (tend evecrgb) hint at something reasonable, but the FA is
*really* low.

Thoughts?

gamma=4258;     % [Hz/g]

t_rise= 0.400e-3;  % Gradient rise time        [s]
delta = 4.600e-3;  % Gradient plateau duration [s]
Delta =12.000e-3;  % Gradient separation time  [s]

% Gradient vectors [Gauss/cm]
G=[ 4.000,   4.000,   4.000;
   15.000,  15.000,   4.000;
   15.000,   4.000,  15.000;
    4.000,  15.000,  15.000;
  -15.000,  15.000,   4.000;
   15.000,   4.000, -15.000;
    4.000, -15.000,  15.000;
   13.000,  12.000,  12.000;
  -13.000,  12.000,  12.000;
   13.000, -12.000,  12.000;
   13.000,  12.000, -12.000;
  -13.000, -12.000,  12.000;
  -13.000,  12.000, -12.000;
   13.000, -12.000, -12.000;
   21.000,   4.000,   4.000;
    4.000,   4.000,  21.000;
    4.000,  21.000,   4.000];

[Teem-users] B-matrix and B-value

[Daniel Ennis <dbe@st...>]

Hi - I've got a rather screwy DTMRI dataset that I'm trying to recon  
with tend estim.  I have been provided with the image data and also  
the diffusion gradient encoding information that is contained below.   
I'm a bit confused as to how tend should use this info to obtain the  
b-matrix and the nominal b-value.

Right now I am simply doing:

tend bmat -i $DNAME -o $BNAME

in order to create the b-matrix and then I'm using an nominal b-value  
of 1000 to which the gradients (below) grossly correspond to.  Where  
$DNAME is a text file with the gradient directions as written below.

I guess the real question is how do we properly handle non-constant b- 
values?  The gradients below have b-values in the range of ~110 to  
~1770 and there is no b-value=0 dataset.  There is a comment in tend  
bmat about not needing to normalize the gradient vector directions,  
but clearly the b-value we pass to tend estim must stand in relation  
to gradients we used.  Which b-value should I be using?

In the end, to estimate the tensors I'm using the following:

tend bmat -i $DNAME -o $BNAME

The results (tend evecrgb) hint and something reasonable, but the FA  
is *really* low.

Thoughts?

> gamma=4258;     % [Hz/g]
>
> t_rise= 0.400e-3;  % Gradient rise time        [s]
> delta = 4.600e-3;  % Gradient plateau duration [s]
> Delta =12.000e-3;  % Gradient separation time  [s]
>
> % Gradient vectors [Gauss/cm]
> G=[ 4.000,   4.000,   4.000;
>    15.000,  15.000,   4.000;
>    15.000,   4.000,  15.000;
>     4.000,  15.000,  15.000;
>   -15.000,  15.000,   4.000;
>    15.000,   4.000, -15.000;
>     4.000, -15.000,  15.000;
>    13.000,  12.000,  12.000;
>   -13.000,  12.000,  12.000;
>    13.000, -12.000,  12.000;
>    13.000,  12.000, -12.000;
>   -13.000, -12.000,  12.000;
>   -13.000,  12.000, -12.000;
>    13.000, -12.000, -12.000;
>    21.000,   4.000,   4.000;
>     4.000,   4.000,  21.000;
>     4.000,  21.000,   4.000];


--
Daniel B. Ennis, Ph.D.
Assistant Professor
University of California, Los Angeles
David Geffen School of Medicine
Department of Radiological Sciences
Diagnostic Cardiovascular Imaging

Re: [Teem-users] How to save a nrrd complete with comments?

[J. Davison de St. Germain <dav@sc...>]

Hi,
  I should have been a little more clear.  I'm trying to do this 
programmatically using nrrdSave().
      - Davison

J. Davison de St. Germain wrote:
> Hi,
>
>    I'm creating a new nrrd from an old nrrd, and would like to get the 
> comments that are saved in the old nrrd's header placed into the new 
> nrrd's header.  Can someone tell me how to go about doing this?
>
>     Thanks,
>                Davison
>
>   

-- 
-----------------------------------------------------------------------
- J. Davison de St. Germain         dav@...    (801) 581-4078 -
- Chief Software Engineer           http://www.cs.utah.edu/~dav       -
- SCI Institute, SE C-SAFE          University of Utah                -
-----------------------------------------------------------------------

[Teem-users] How to save a nrrd complete with comments?

[J. Davison de St. Germain <dav@sc...>]

Hi,

   I'm creating a new nrrd from an old nrrd, and would like to get the 
comments that are saved in the old nrrd's header placed into the new 
nrrd's header.  Can someone tell me how to go about doing this?

    Thanks,
               Davison

-- 
-----------------------------------------------------------------------
- J. Davison de St. Germain         dav@...    (801) 581-4078 -
- Chief Software Engineer           http://www.cs.utah.edu/~dav       -
- SCI Institute, SE C-SAFE          University of Utah                -
-----------------------------------------------------------------------

Re: [Teem-users] reconstructing diffusion tensors

[James Bigler <jamesbigler@gm...>]

You should be able to specify which axis you wish to join on.

I would try this after you make all your nrrds:

unu join -a 0 -incr -i tensor{0,1,2,3,4,5}.nrrd

This tells it to join along the fastest axis (-a 0) and scissor the
nrrds together.  "-incr" will add an extra dimension so that your new
nrrd will be 6x256x256x30.

James

On Fri, Aug 15, 2008 at 6:50 AM, Jimmy Yang <mjyang.jimmy@...> wrote:
> Hi,
>
> I'm relatively new to the Teem library but am quickly becoming a big fan.  I
> have a rather simple and (probably silly) question.  I'm currently working
> with diffusion tensor data, but the components of the diffusion tensor are
> separated into 6 separate files, ie. each file is 256x256x30 array of scalar
> values, each representing either Dxx, Dxy, etc.  I was wondering if there
> was any command - line function in unu/tend that could combine those 6 files
> into one?  My understanding of unu join is that it will connect the files
> end to end, which isn't quite what I'm looking for.
>
> Thank you!
>
> Jimmy Yang
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> teem-users mailing list
> teem-users@...
> https://lists.sourceforge.net/lists/listinfo/teem-users
>
>

[Teem-users] reconstructing diffusion tensor matrix

[Jimmy Yang <mjyang.jimmy@gm...>]

Hi,

I'm relatively new to the Teem library but am quickly becoming a big fan.  I
have a rather simple and (probably silly) question.  I'm currently working
with diffusion tensor data, but the components of the diffusion tensor are
separated into 6 separate files, ie. each file is 256x256x30 array of scalar
values, each representing either Dxx, Dxy, etc.  I was wondering if there
was any command - line function in unu/tend that could combine those 6 files
into one?  My understanding of unu join is that it will connect the files
end to end, which isn't quite what I'm looking for.

Thank you!

Jimmy Yang

[Teem-users] reconstructing diffusion tensors

[Jimmy Yang <mjyang.jimmy@gm...>]

Hi,

I'm relatively new to the Teem library but am quickly becoming a big fan.  I
have a rather simple and (probably silly) question.  I'm currently working
with diffusion tensor data, but the components of the diffusion tensor are
separated into 6 separate files, ie. each file is 256x256x30 array of scalar
values, each representing either Dxx, Dxy, etc.  I was wondering if there
was any command - line function in unu/tend that could combine those 6 files
into one?  My understanding of unu join is that it will connect the files
end to end, which isn't quite what I'm looking for.

Thank you!

Jimmy Yang

Re: [Teem-users] teem-users Digest, Vol 23, Issue 5

[James Bigler <jamesbigler@gm...>]

On Tue, Aug 12, 2008 at 8:46 AM, Daniel Ennis <dbe@...> wrote:
> So, I ultimately used the "export TEEM_ZLIB=1" approach and everything
> appears to be fine.  Thanks all!
> I appreciate the updates that Gordon made, but for me, at least, they are
> still incomplete (sorry Gordon!).  I'm not a hacker, and my
> coding abilities are rather pedestrian compared to the average
> all-night-coder.  Perhaps, there should be more language so that non-hackers
> can still become users.  I would suggest including some of the original
> "make" directions (i.e. Download the teem distribution etc.) and then
> directions on using CMake.  I still don't know what to do at the terminal!
> -Dan-

Would an installable nightly help this issue at all?  I'm not sure
what that would entail, but it might be a compromise between using 1.9
and SVN HEAD.

James

Re: [Teem-users] teem-users Digest, Vol 23, Issue 5

[Gordon Kindlmann <gk@bw...>]

hi-

Okay, I've updated the info here:

http://teem.sourceforge.net/build.html

to reflect the fact that CMake is the (new) way to go, and there are  
links to the CMake website.

I'm sorry for the confusion.

Dan- let me know if you're able to get CMake working.

Gordon

On Aug 12, 2008, at 1:10 AM, John C. Anderson wrote:

> The first time I tried to build teem w/ optional libraries I did an
> "export TEEM_ZLIB" rather than "export TEEM_ZLIB=1" as well.  Perhaps
> this sentence in the build instructions should be changed to hint at
> what to do for Bourne-style shells?
>
> "The following three variables need simply to be set (as with "setenv
> TEEM_ZLIB"), as opposed to set to a specific string (as with "setenv
> TEEM_ZLIB true"):"
>
> Maybe to:
>
> "The following three variables need simply to be set, as with: "setenv
> TEEM_ZLIB" for csh-style shells, or "export TEEM_ZLIB=1" for sh-style
> shells:"
>
> John
>
>
> On Aug 11, 2008, at 9:56 PM, Daniel Ennis wrote:
>
>> Perhaps my problem, in part, is indicative of documentation  
>> issues, my
>> own pedestrian abilities, or both.
>>
>> I'll try the other options when I'm back at my desktop, but can
>> someone point me to more info about using Cmake?
>>
>> --
>> Daniel Ennis, Ph.D
>> Assistant Professor
>> University of California, Los Angeles
>> David Geffen School of Medicine
>> Department of Radiological Sciences
>> Diagnostic Cardiovascular Imaging
>>
>> On Aug 11, 2008, at 20:15, teem-users-request@...
>> wrote:
>>
>>> Send teem-users mailing list submissions to
>>>   teem-users@...
>>>
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>   https://lists.sourceforge.net/lists/listinfo/teem-users
>>> or, via email, send a message with subject or body 'help' to
>>>   teem-users-request@...
>>>
>>> You can reach the person managing the list at
>>>   teem-users-owner@...
>>>
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of teem-users digest..."
>>>
>>>
>>> Today's Topics:
>>>
>>>  1. Re: unu join segmentation fault (Gordon Kindlmann)
>>>  2. Building TEEM (darwin.64 specific?) (Daniel Ennis)
>>>  3. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>>>  4. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>>>  5. Re: Building TEEM (darwin.64 specific?) (Xavier Tricoche)
>>>
>>>
>>> -------------------------------------------------------------------- 
>>> --
>>>
>>> Message: 1
>>> Date: Mon, 11 Aug 2008 17:04:13 -0400
>>> From: Gordon Kindlmann <gk@...>
>>> Subject: Re: [Teem-users] unu join segmentation fault
>>> To: Anastasia Mironova <mironova@...>
>>> Cc: teem-users@...
>>> Message-ID: <E05E23F2-14FC-4DC6-A86F-0202C69AD955@...>
>>> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>>>
>>> Hello-
>>>
>>> Thanks for debugging the issue as much as you did.
>>>
>>> Can you put the files online?
>>>
>>> Also, are you using the latest SVN checkout?
>>>
>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>>
>>> Gordon
>>>
>>> On Aug 11, 2008, at 12:47 PM, Anastasia Mironova wrote:
>>>
>>>> Hello All,
>>>>
>>>> I am getting a Segmentation Fault out of
>>>>
>>>> unu join -i normal0/mean.nrrd normal1/mean.nrrd -a 0 | unu
>>>> save -f nrrd -e ascii -i - -o mean.nhdr
>>>>
>>>> I have tried the following:
>>>> - used the unu join command with other files - works
>>>> - used unu minmax command on both input files - works
>>>> - used more on both input files - works
>>>> - saved those files into a different format - doesn't help
>>>> - saved those files into a different directory - doesn't
>>>> help
>>>> - used unu to write a sample test file into the current
>>>> directory to test writing issues - works
>>>> - space is not an issue - there's 53 GB available...
>>>> - tried running it on different machines and as different
>>>> users - doesnt' work either
>>>>
>>>> PLEASE HELP!...
>>>>
>>>> Thanks so much!
>>>> -Anastasia
>>>>
>>>>
>>>> ---
>>>> -------------------------------------------------------------------
>>>> ---
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>> challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>> great prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in
>>>> the world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>> _______________________________________________
>>>> teem-users mailing list
>>>> teem-users@...
>>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Mon, 11 Aug 2008 19:50:10 -0700
>>> From: Daniel Ennis <dbe@...>
>>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>> To: teem-users@...
>>> Cc: Daniel Ennis <dbe@...>
>>> Message-ID: <823F61C6-9F5E-47AB-8A11-D12E170132D1@...>
>>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>>
>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>> trouble
>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>> there
>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>> mistakes in the following?  I started out with:
>>>
>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>>
>>> Into /Users/dbe/bin/
>>>
>>> Then...
>>>
>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>> that reads:
>>>
>>> TEEM_ENDIAN = 4321
>>>
>>> to
>>>
>>> TEEM_ENDIAN = 1234
>>>
>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>> Apple), which stuffs everything into /opt/local/
>>>
>>>   http://www.macports.org/install.php
>>>
>>>   -OR-
>>>
>>>   http://guide.macports.org/
>>>
>>>
>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>
>>>   i) sudo port install zlib
>>>
>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>
>>>   i) sudo port install bzip2
>>>
>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>
>>>   i) sudo port install libpng
>>>
>>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>>> but TEEM won't know where to find it unless you do this...
>>>
>>>   export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>   export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>   export TEEM_PNG_IPATH=-I/opt/local/include
>>>
>>>   export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>   export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>   export TEEM_PNG_HPATH=-L/opt/local/lib
>>>
>>> G) Finally,
>>>
>>>   cd /Users/dbe/bin/teem/src/
>>>   export TEEM_ZLIB
>>>   export TEEM_BZIP2
>>>   export TEEM_PNG
>>>   export TEEM_ARCH=darwin.64
>>>
>>>   make clobber; make;
>>>
>>>   cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>
>>> The last step reports:
>>>
>>> ./nrrdSanity: nrrd sanity check passed.
>>>
>>> ./nrrdSanity: encodings supported in this build:
>>> raw: yes
>>> ascii: yes
>>> hex: yes
>>> gz: not available
>>> bz2: not available
>>> ./nrrdSanity: formats supported in this build:
>>> nrrd: yes
>>> pnm: yes
>>> png: not available
>>> vtk: yes
>>> text: yes
>>> eps: yes
>>>
>>>
>>> Thanks!
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 3
>>> Date: Mon, 11 Aug 2008 20:00:49 -0700
>>> From: "Amit Chourasia" <amit@...>
>>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>>> To: "Daniel Ennis" <dbe@...>,
>>>   <teem-users@...>
>>> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2948@...>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Daniel,
>>>
>>> Add the following before running make and see if it works
>>>
>>> export TEEM_EXT=1
>>> export TEEM_PNG=1
>>> export TEEM_ZLIB=1
>>>
>>> --Amit
>>>
>>>
>>> -----Original Message-----
>>> From: teem-users-bounces@... on behalf of Daniel
>>> Ennis
>>> Sent: Mon 8/11/2008 7:50 PM
>>> To: teem-users@...
>>> Cc: Daniel Ennis
>>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>>
>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>> trouble
>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>> there
>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>> mistakes in the following?  I started out with:
>>>
>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>>
>>> Into /Users/dbe/bin/
>>>
>>> Then...
>>>
>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>> that reads:
>>>
>>> TEEM_ENDIAN = 4321
>>>
>>> to
>>>
>>> TEEM_ENDIAN = 1234
>>>
>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>> Apple), which stuffs everything into /opt/local/
>>>
>>>   http://www.macports.org/install.php
>>>
>>>   -OR-
>>>
>>>   http://guide.macports.org/
>>>
>>>
>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>
>>>   i) sudo port install zlib
>>>
>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>
>>>   i) sudo port install bzip2
>>>
>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>
>>>   i) sudo port install libpng
>>>
>>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>>> but TEEM won't know where to find it unless you do this...
>>>
>>>   export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>   export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>   export TEEM_PNG_IPATH=-I/opt/local/include
>>>
>>>   export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>   export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>   export TEEM_PNG_HPATH=-L/opt/local/lib
>>>
>>> G) Finally,
>>>
>>>   cd /Users/dbe/bin/teem/src/
>>>   export TEEM_ZLIB
>>>   export TEEM_BZIP2
>>>   export TEEM_PNG
>>>   export TEEM_ARCH=darwin.64
>>>
>>>   make clobber; make;
>>>
>>>   cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>
>>> The last step reports:
>>>
>>> ./nrrdSanity: nrrd sanity check passed.
>>>
>>> ./nrrdSanity: encodings supported in this build:
>>> raw: yes
>>> ascii: yes
>>> hex: yes
>>> gz: not available
>>> bz2: not available
>>> ./nrrdSanity: formats supported in this build:
>>> nrrd: yes
>>> pnm: yes
>>> png: not available
>>> vtk: yes
>>> text: yes
>>> eps: yes
>>>
>>>
>>> Thanks!
>>>
>>> ---
>>> -------------------------------------------------------------------- 
>>> --
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> teem-users mailing list
>>> teem-users@...
>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>>
>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Mon, 11 Aug 2008 20:04:07 -0700
>>> From: "Amit Chourasia" <amit@...>
>>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>>> To: "Daniel Ennis" <dbe@...>,
>>>   <teem-users@...>
>>> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2949@...>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Also, make sure all the dependent libraries(zlib, png, bzip2) are
>>> built in 64 bit.
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: teem-users-bounces@... on behalf of Daniel
>>> Ennis
>>> Sent: Mon 8/11/2008 7:50 PM
>>> To: teem-users@...
>>> Cc: Daniel Ennis
>>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>>
>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>> trouble
>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>> there
>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>> mistakes in the following?  I started out with:
>>>
>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>>
>>> Into /Users/dbe/bin/
>>>
>>> Then...
>>>
>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>> that reads:
>>>
>>> TEEM_ENDIAN = 4321
>>>
>>> to
>>>
>>> TEEM_ENDIAN = 1234
>>>
>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>> Apple), which stuffs everything into /opt/local/
>>>
>>>   http://www.macports.org/install.php
>>>
>>>   -OR-
>>>
>>>   http://guide.macports.org/
>>>
>>>
>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>
>>>   i) sudo port install zlib
>>>
>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>
>>>   i) sudo port install bzip2
>>>
>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>
>>>   i) sudo port install libpng
>>>
>>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>>> but TEEM won't know where to find it unless you do this...
>>>
>>>   export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>   export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>   export TEEM_PNG_IPATH=-I/opt/local/include
>>>
>>>   export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>   export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>   export TEEM_PNG_HPATH=-L/opt/local/lib
>>>
>>> G) Finally,
>>>
>>>   cd /Users/dbe/bin/teem/src/
>>>   export TEEM_ZLIB
>>>   export TEEM_BZIP2
>>>   export TEEM_PNG
>>>   export TEEM_ARCH=darwin.64
>>>
>>>   make clobber; make;
>>>
>>>   cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>
>>> The last step reports:
>>>
>>> ./nrrdSanity: nrrd sanity check passed.
>>>
>>> ./nrrdSanity: encodings supported in this build:
>>> raw: yes
>>> ascii: yes
>>> hex: yes
>>> gz: not available
>>> bz2: not available
>>> ./nrrdSanity: formats supported in this build:
>>> nrrd: yes
>>> pnm: yes
>>> png: not available
>>> vtk: yes
>>> text: yes
>>> eps: yes
>>>
>>>
>>> Thanks!
>>>
>>> ---
>>> -------------------------------------------------------------------- 
>>> --
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> teem-users mailing list
>>> teem-users@...
>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>>
>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Mon, 11 Aug 2008 20:15:00 -0700
>>> From: Xavier Tricoche <tricoche@...>
>>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>>> To: Daniel Ennis <dbe@...>
>>> Cc: Daniel Ennis <dbe@...>,
>>>   "teem-users@..." <teem-
>>> users@...
>>>>
>>> Message-ID: <397A9647-CF41-4328-A877-9A0BFF126AE6@...>
>>> Content-Type: text/plain;    charset=us-ascii;    format=flowed;
>>> delsp=yes
>>>
>>> Hi,
>>>
>>> I found CMake to take the pain out of it. Any good reason not to use
>>> it?
>>>
>>> Xavier
>>>
>>> Sent from my iPhone
>>>
>>> On Aug 11, 2008, at 7:50 PM, Daniel Ennis <dbe@...> wrote:
>>>
>>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>>> trouble
>>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>>> there
>>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>>> mistakes in the following?  I started out with:
>>>>
>>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk  
>>>> teem
>>>>
>>>> Into /Users/dbe/bin/
>>>>
>>>> Then...
>>>>
>>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>>> that reads:
>>>>
>>>> TEEM_ENDIAN = 4321
>>>>
>>>> to
>>>>
>>>> TEEM_ENDIAN = 1234
>>>>
>>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>>> Apple), which stuffs everything into /opt/local/
>>>>
>>>>  http://www.macports.org/install.php
>>>>
>>>>  -OR-
>>>>
>>>>  http://guide.macports.org/
>>>>
>>>>
>>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>>
>>>>  i) sudo port install zlib
>>>>
>>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>>
>>>>  i) sudo port install bzip2
>>>>
>>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>>
>>>>  i) sudo port install libpng
>>>>
>>>> F) All of the Mac Ports stuff is installed in /opt/local/be  
>>>> default,
>>>> but TEEM won't know where to find it unless you do this...
>>>>
>>>>  export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>>  export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>>  export TEEM_PNG_IPATH=-I/opt/local/include
>>>>
>>>>  export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>>  export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>>  export TEEM_PNG_HPATH=-L/opt/local/lib
>>>>
>>>> G) Finally,
>>>>
>>>>  cd /Users/dbe/bin/teem/src/
>>>>  export TEEM_ZLIB
>>>>  export TEEM_BZIP2
>>>>  export TEEM_PNG
>>>>  export TEEM_ARCH=darwin.64
>>>>
>>>>  make clobber; make;
>>>>
>>>>  cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>>
>>>> The last step reports:
>>>>
>>>> ./nrrdSanity: nrrd sanity check passed.
>>>>
>>>> ./nrrdSanity: encodings supported in this build:
>>>> raw: yes
>>>> ascii: yes
>>>> hex: yes
>>>> gz: not available
>>>> bz2: not available
>>>> ./nrrdSanity: formats supported in this build:
>>>> nrrd: yes
>>>> pnm: yes
>>>> png: not available
>>>> vtk: yes
>>>> text: yes
>>>> eps: yes
>>>>
>>>>
>>>> Thanks!
>>>>
>>>> ---
>>>> ---
>>>> -------------------------------------------------------------------
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>> challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>> great prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in
>>>> the world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>> _______________________________________________
>>>> teem-users mailing list
>>>> teem-users@...
>>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> ---
>>> -------------------------------------------------------------------- 
>>> --
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> teem-users mailing list
>>> teem-users@...
>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>
>>>
>>> End of teem-users Digest, Vol 23, Issue 5
>>> *****************************************
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> teem-users mailing list
> teem-users@...
> https://lists.sourceforge.net/lists/listinfo/teem-users

Re: [Teem-users] teem-users Digest, Vol 23, Issue 5

[Daniel Ennis <dbe@st...>]

So, I ultimately used the "export TEEM_ZLIB=1" approach and everything  
appears to be fine.  Thanks all!

I appreciate the updates that Gordon made, but for me, at least, they  
are still incomplete (sorry Gordon!).  I'm not a hacker, and my coding  
abilities are rather pedestrian compared to the average all-night- 
coder.  Perhaps, there should be more language so that non-hackers can  
still become users.  I would suggest including some of the original  
"make" directions (i.e. Download the teem distribution etc.) and then  
directions on using CMake.  I still don't know what to do at the  
terminal!

		-Dan-

On Aug 12, 2008, at 8:24 AM, Gordon Kindlmann wrote:

> hi-
>
> Okay, I've updated the info here:
>
> http://teem.sourceforge.net/build.html
>
> to reflect the fact that CMake is the (new) way to go, and there are  
> links to the CMake website.
>
> I'm sorry for the confusion.
>
> Dan- let me know if you're able to get CMake working.
>
> Gordon
>
> On Aug 12, 2008, at 1:10 AM, John C. Anderson wrote:
>
>> The first time I tried to build teem w/ optional libraries I did an
>> "export TEEM_ZLIB" rather than "export TEEM_ZLIB=1" as well.  Perhaps
>> this sentence in the build instructions should be changed to hint at
>> what to do for Bourne-style shells?
>>
>> "The following three variables need simply to be set (as with "setenv
>> TEEM_ZLIB"), as opposed to set to a specific string (as with "setenv
>> TEEM_ZLIB true"):"
>>
>> Maybe to:
>>
>> "The following three variables need simply to be set, as with:  
>> "setenv
>> TEEM_ZLIB" for csh-style shells, or "export TEEM_ZLIB=1" for sh-style
>> shells:"
>>
>> John
>>
>>
>> On Aug 11, 2008, at 9:56 PM, Daniel Ennis wrote:
>>
>>> Perhaps my problem, in part, is indicative of documentation  
>>> issues, my
>>> own pedestrian abilities, or both.
>>>
>>> I'll try the other options when I'm back at my desktop, but can
>>> someone point me to more info about using Cmake?
>>>
>>> --
>>> Daniel Ennis, Ph.D
>>> Assistant Professor
>>> University of California, Los Angeles
>>> David Geffen School of Medicine
>>> Department of Radiological Sciences
>>> Diagnostic Cardiovascular Imaging
>>>
>>> On Aug 11, 2008, at 20:15, teem-users-request@...
>>> wrote:
>>>
>>>> Send teem-users mailing list submissions to
>>>>  teem-users@...
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>  https://lists.sourceforge.net/lists/listinfo/teem-users
>>>> or, via email, send a message with subject or body 'help' to
>>>>  teem-users-request@...
>>>>
>>>> You can reach the person managing the list at
>>>>  teem-users-owner@...
>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of teem-users digest..."
>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. Re: unu join segmentation fault (Gordon Kindlmann)
>>>> 2. Building TEEM (darwin.64 specific?) (Daniel Ennis)
>>>> 3. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>>>> 4. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>>>> 5. Re: Building TEEM (darwin.64 specific?) (Xavier Tricoche)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Mon, 11 Aug 2008 17:04:13 -0400
>>>> From: Gordon Kindlmann <gk@...>
>>>> Subject: Re: [Teem-users] unu join segmentation fault
>>>> To: Anastasia Mironova <mironova@...>
>>>> Cc: teem-users@...
>>>> Message-ID: <E05E23F2-14FC-4DC6-A86F-0202C69AD955@...>
>>>> Content-Type: text/plain; charset=US-ASCII; delsp=yes;  
>>>> format=flowed
>>>>
>>>> Hello-
>>>>
>>>> Thanks for debugging the issue as much as you did.
>>>>
>>>> Can you put the files online?
>>>>
>>>> Also, are you using the latest SVN checkout?
>>>>
>>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk  
>>>> teem
>>>>
>>>> Gordon
>>>>
>>>> On Aug 11, 2008, at 12:47 PM, Anastasia Mironova wrote:
>>>>
>>>>> Hello All,
>>>>>
>>>>> I am getting a Segmentation Fault out of
>>>>>
>>>>> unu join -i normal0/mean.nrrd normal1/mean.nrrd -a 0 | unu
>>>>> save -f nrrd -e ascii -i - -o mean.nhdr
>>>>>
>>>>> I have tried the following:
>>>>> - used the unu join command with other files - works
>>>>> - used unu minmax command on both input files - works
>>>>> - used more on both input files - works
>>>>> - saved those files into a different format - doesn't help
>>>>> - saved those files into a different directory - doesn't
>>>>> help
>>>>> - used unu to write a sample test file into the current
>>>>> directory to test writing issues - works
>>>>> - space is not an issue - there's 53 GB available...
>>>>> - tried running it on different machines and as different
>>>>> users - doesnt' work either
>>>>>
>>>>> PLEASE HELP!...
>>>>>
>>>>> Thanks so much!
>>>>> -Anastasia
>>>>>
>>>>>
>>>>> ---
>>>>> -------------------------------------------------------------------
>>>>> ---
>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>> challenge
>>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>>> great prizes
>>>>> Grand prize is a trip for two to an Open Source event anywhere in
>>>>> the world
>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>>> _______________________________________________
>>>>> teem-users mailing list
>>>>> teem-users@...
>>>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Mon, 11 Aug 2008 19:50:10 -0700
>>>> From: Daniel Ennis <dbe@...>
>>>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>>> To: teem-users@...
>>>> Cc: Daniel Ennis <dbe@...>
>>>> Message-ID: <823F61C6-9F5E-47AB-8A11-D12E170132D1@...>
>>>> Content-Type: text/plain; charset=US-ASCII; format=flowed;  
>>>> delsp=yes
>>>>
>>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>>> trouble
>>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>>> there
>>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>>> mistakes in the following?  I started out with:
>>>>
>>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk  
>>>> teem
>>>>
>>>> Into /Users/dbe/bin/
>>>>
>>>> Then...
>>>>
>>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>>> that reads:
>>>>
>>>> TEEM_ENDIAN = 4321
>>>>
>>>> to
>>>>
>>>> TEEM_ENDIAN = 1234
>>>>
>>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>>> Apple), which stuffs everything into /opt/local/
>>>>
>>>>  http://www.macports.org/install.php
>>>>
>>>>  -OR-
>>>>
>>>>  http://guide.macports.org/
>>>>
>>>>
>>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>>
>>>>  i) sudo port install zlib
>>>>
>>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>>
>>>>  i) sudo port install bzip2
>>>>
>>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>>
>>>>  i) sudo port install libpng
>>>>
>>>> F) All of the Mac Ports stuff is installed in /opt/local/be  
>>>> default,
>>>> but TEEM won't know where to find it unless you do this...
>>>>
>>>>  export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>>  export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>>  export TEEM_PNG_IPATH=-I/opt/local/include
>>>>
>>>>  export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>>  export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>>  export TEEM_PNG_HPATH=-L/opt/local/lib
>>>>
>>>> G) Finally,
>>>>
>>>>  cd /Users/dbe/bin/teem/src/
>>>>  export TEEM_ZLIB
>>>>  export TEEM_BZIP2
>>>>  export TEEM_PNG
>>>>  export TEEM_ARCH=darwin.64
>>>>
>>>>  make clobber; make;
>>>>
>>>>  cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>>
>>>> The last step reports:
>>>>
>>>> ./nrrdSanity: nrrd sanity check passed.
>>>>
>>>> ./nrrdSanity: encodings supported in this build:
>>>> raw: yes
>>>> ascii: yes
>>>> hex: yes
>>>> gz: not available
>>>> bz2: not available
>>>> ./nrrdSanity: formats supported in this build:
>>>> nrrd: yes
>>>> pnm: yes
>>>> png: not available
>>>> vtk: yes
>>>> text: yes
>>>> eps: yes
>>>>
>>>>
>>>> Thanks!
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Mon, 11 Aug 2008 20:00:49 -0700
>>>> From: "Amit Chourasia" <amit@...>
>>>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>>>> To: "Daniel Ennis" <dbe@...>,
>>>>  <teem-users@...>
>>>> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2948@...>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> Daniel,
>>>>
>>>> Add the following before running make and see if it works
>>>>
>>>> export TEEM_EXT=1
>>>> export TEEM_PNG=1
>>>> export TEEM_ZLIB=1
>>>>
>>>> --Amit
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: teem-users-bounces@... on behalf of Daniel
>>>> Ennis
>>>> Sent: Mon 8/11/2008 7:50 PM
>>>> To: teem-users@...
>>>> Cc: Daniel Ennis
>>>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>>>
>>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>>> trouble
>>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>>> there
>>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>>> mistakes in the following?  I started out with:
>>>>
>>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk  
>>>> teem
>>>>
>>>> Into /Users/dbe/bin/
>>>>
>>>> Then...
>>>>
>>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>>> that reads:
>>>>
>>>> TEEM_ENDIAN = 4321
>>>>
>>>> to
>>>>
>>>> TEEM_ENDIAN = 1234
>>>>
>>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>>> Apple), which stuffs everything into /opt/local/
>>>>
>>>>  http://www.macports.org/install.php
>>>>
>>>>  -OR-
>>>>
>>>>  http://guide.macports.org/
>>>>
>>>>
>>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>>
>>>>  i) sudo port install zlib
>>>>
>>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>>
>>>>  i) sudo port install bzip2
>>>>
>>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>>
>>>>  i) sudo port install libpng
>>>>
>>>> F) All of the Mac Ports stuff is installed in /opt/local/be  
>>>> default,
>>>> but TEEM won't know where to find it unless you do this...
>>>>
>>>>  export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>>  export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>>  export TEEM_PNG_IPATH=-I/opt/local/include
>>>>
>>>>  export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>>  export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>>  export TEEM_PNG_HPATH=-L/opt/local/lib
>>>>
>>>> G) Finally,
>>>>
>>>>  cd /Users/dbe/bin/teem/src/
>>>>  export TEEM_ZLIB
>>>>  export TEEM_BZIP2
>>>>  export TEEM_PNG
>>>>  export TEEM_ARCH=darwin.64
>>>>
>>>>  make clobber; make;
>>>>
>>>>  cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>>
>>>> The last step reports:
>>>>
>>>> ./nrrdSanity: nrrd sanity check passed.
>>>>
>>>> ./nrrdSanity: encodings supported in this build:
>>>> raw: yes
>>>> ascii: yes
>>>> hex: yes
>>>> gz: not available
>>>> bz2: not available
>>>> ./nrrdSanity: formats supported in this build:
>>>> nrrd: yes
>>>> pnm: yes
>>>> png: not available
>>>> vtk: yes
>>>> text: yes
>>>> eps: yes
>>>>
>>>>
>>>> Thanks!
>>>>
>>>> ---
>>>> ----------------------------------------------------------------------
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>> challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>> great prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in
>>>> the world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>> _______________________________________________
>>>> teem-users mailing list
>>>> teem-users@...
>>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 4
>>>> Date: Mon, 11 Aug 2008 20:04:07 -0700
>>>> From: "Amit Chourasia" <amit@...>
>>>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>>>> To: "Daniel Ennis" <dbe@...>,
>>>>  <teem-users@...>
>>>> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2949@...>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> Also, make sure all the dependent libraries(zlib, png, bzip2) are
>>>> built in 64 bit.
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: teem-users-bounces@... on behalf of Daniel
>>>> Ennis
>>>> Sent: Mon 8/11/2008 7:50 PM
>>>> To: teem-users@...
>>>> Cc: Daniel Ennis
>>>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>>>
>>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>>> trouble
>>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>>> there
>>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>>> mistakes in the following?  I started out with:
>>>>
>>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk  
>>>> teem
>>>>
>>>> Into /Users/dbe/bin/
>>>>
>>>> Then...
>>>>
>>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>>> that reads:
>>>>
>>>> TEEM_ENDIAN = 4321
>>>>
>>>> to
>>>>
>>>> TEEM_ENDIAN = 1234
>>>>
>>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>>> Apple), which stuffs everything into /opt/local/
>>>>
>>>>  http://www.macports.org/install.php
>>>>
>>>>  -OR-
>>>>
>>>>  http://guide.macports.org/
>>>>
>>>>
>>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>>
>>>>  i) sudo port install zlib
>>>>
>>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>>
>>>>  i) sudo port install bzip2
>>>>
>>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>>
>>>>  i) sudo port install libpng
>>>>
>>>> F) All of the Mac Ports stuff is installed in /opt/local/be  
>>>> default,
>>>> but TEEM won't know where to find it unless you do this...
>>>>
>>>>  export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>>  export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>>  export TEEM_PNG_IPATH=-I/opt/local/include
>>>>
>>>>  export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>>  export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>>  export TEEM_PNG_HPATH=-L/opt/local/lib
>>>>
>>>> G) Finally,
>>>>
>>>>  cd /Users/dbe/bin/teem/src/
>>>>  export TEEM_ZLIB
>>>>  export TEEM_BZIP2
>>>>  export TEEM_PNG
>>>>  export TEEM_ARCH=darwin.64
>>>>
>>>>  make clobber; make;
>>>>
>>>>  cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>>
>>>> The last step reports:
>>>>
>>>> ./nrrdSanity: nrrd sanity check passed.
>>>>
>>>> ./nrrdSanity: encodings supported in this build:
>>>> raw: yes
>>>> ascii: yes
>>>> hex: yes
>>>> gz: not available
>>>> bz2: not available
>>>> ./nrrdSanity: formats supported in this build:
>>>> nrrd: yes
>>>> pnm: yes
>>>> png: not available
>>>> vtk: yes
>>>> text: yes
>>>> eps: yes
>>>>
>>>>
>>>> Thanks!
>>>>
>>>> ---
>>>> ----------------------------------------------------------------------
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>> challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>> great prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in
>>>> the world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>> _______________________________________________
>>>> teem-users mailing list
>>>> teem-users@...
>>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 5
>>>> Date: Mon, 11 Aug 2008 20:15:00 -0700
>>>> From: Xavier Tricoche <tricoche@...>
>>>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>>>> To: Daniel Ennis <dbe@...>
>>>> Cc: Daniel Ennis <dbe@...>,
>>>>  "teem-users@..." <teem-
>>>> users@...
>>>>>
>>>> Message-ID: <397A9647-CF41-4328-A877-9A0BFF126AE6@...>
>>>> Content-Type: text/plain;    charset=us-ascii;    format=flowed;
>>>> delsp=yes
>>>>
>>>> Hi,
>>>>
>>>> I found CMake to take the pain out of it. Any good reason not to  
>>>> use
>>>> it?
>>>>
>>>> Xavier
>>>>
>>>> Sent from my iPhone
>>>>
>>>> On Aug 11, 2008, at 7:50 PM, Daniel Ennis <dbe@...> wrote:
>>>>
>>>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>>>> trouble
>>>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>>>> there
>>>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>>>> mistakes in the following?  I started out with:
>>>>>
>>>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk  
>>>>> teem
>>>>>
>>>>> Into /Users/dbe/bin/
>>>>>
>>>>> Then...
>>>>>
>>>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>>>> that reads:
>>>>>
>>>>> TEEM_ENDIAN = 4321
>>>>>
>>>>> to
>>>>>
>>>>> TEEM_ENDIAN = 1234
>>>>>
>>>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>>>> Apple), which stuffs everything into /opt/local/
>>>>>
>>>>> http://www.macports.org/install.php
>>>>>
>>>>> -OR-
>>>>>
>>>>> http://guide.macports.org/
>>>>>
>>>>>
>>>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>>>
>>>>> i) sudo port install zlib
>>>>>
>>>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>>>
>>>>> i) sudo port install bzip2
>>>>>
>>>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>>>
>>>>> i) sudo port install libpng
>>>>>
>>>>> F) All of the Mac Ports stuff is installed in /opt/local/be  
>>>>> default,
>>>>> but TEEM won't know where to find it unless you do this...
>>>>>
>>>>> export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>>> export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>>> export TEEM_PNG_IPATH=-I/opt/local/include
>>>>>
>>>>> export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>>> export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>>> export TEEM_PNG_HPATH=-L/opt/local/lib
>>>>>
>>>>> G) Finally,
>>>>>
>>>>> cd /Users/dbe/bin/teem/src/
>>>>> export TEEM_ZLIB
>>>>> export TEEM_BZIP2
>>>>> export TEEM_PNG
>>>>> export TEEM_ARCH=darwin.64
>>>>>
>>>>> make clobber; make;
>>>>>
>>>>> cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>>>
>>>>> The last step reports:
>>>>>
>>>>> ./nrrdSanity: nrrd sanity check passed.
>>>>>
>>>>> ./nrrdSanity: encodings supported in this build:
>>>>> raw: yes
>>>>> ascii: yes
>>>>> hex: yes
>>>>> gz: not available
>>>>> bz2: not available
>>>>> ./nrrdSanity: formats supported in this build:
>>>>> nrrd: yes
>>>>> pnm: yes
>>>>> png: not available
>>>>> vtk: yes
>>>>> text: yes
>>>>> eps: yes
>>>>>
>>>>>
>>>>> Thanks!
>>>>>
>>>>> ---
>>>>> ---
>>>>> -------------------------------------------------------------------
>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>> challenge
>>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>>> great prizes
>>>>> Grand prize is a trip for two to an Open Source event anywhere in
>>>>> the world
>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>>> _______________________________________________
>>>>> teem-users mailing list
>>>>> teem-users@...
>>>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> ---
>>>> ----------------------------------------------------------------------
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>> challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>> great prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in
>>>> the world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> teem-users mailing list
>>>> teem-users@...
>>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>>>
>>>>
>>>> End of teem-users Digest, Vol 23, Issue 5
>>>> *****************************************
>>>
>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> teem-users mailing list
>>> teem-users@...
>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's  
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win  
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in  
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>

Re: [Teem-users] teem-users Digest, Vol 23, Issue 5

[John C. Anderson <anderson@cs...>]

The first time I tried to build teem w/ optional libraries I did an  
"export TEEM_ZLIB" rather than "export TEEM_ZLIB=1" as well.  Perhaps  
this sentence in the build instructions should be changed to hint at  
what to do for Bourne-style shells?

"The following three variables need simply to be set (as with "setenv  
TEEM_ZLIB"), as opposed to set to a specific string (as with "setenv  
TEEM_ZLIB true"):"

Maybe to:

"The following three variables need simply to be set, as with: "setenv  
TEEM_ZLIB" for csh-style shells, or "export TEEM_ZLIB=1" for sh-style  
shells:"

John


On Aug 11, 2008, at 9:56 PM, Daniel Ennis wrote:

> Perhaps my problem, in part, is indicative of documentation issues, my
> own pedestrian abilities, or both.
>
> I'll try the other options when I'm back at my desktop, but can
> someone point me to more info about using Cmake?
>
> --
> Daniel Ennis, Ph.D
> Assistant Professor
> University of California, Los Angeles
> David Geffen School of Medicine
> Department of Radiological Sciences
> Diagnostic Cardiovascular Imaging
>
> On Aug 11, 2008, at 20:15, teem-users-request@...
> wrote:
>
>> Send teem-users mailing list submissions to
>>   teem-users@...
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>   https://lists.sourceforge.net/lists/listinfo/teem-users
>> or, via email, send a message with subject or body 'help' to
>>   teem-users-request@...
>>
>> You can reach the person managing the list at
>>   teem-users-owner@...
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of teem-users digest..."
>>
>>
>> Today's Topics:
>>
>>  1. Re: unu join segmentation fault (Gordon Kindlmann)
>>  2. Building TEEM (darwin.64 specific?) (Daniel Ennis)
>>  3. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>>  4. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>>  5. Re: Building TEEM (darwin.64 specific?) (Xavier Tricoche)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 11 Aug 2008 17:04:13 -0400
>> From: Gordon Kindlmann <gk@...>
>> Subject: Re: [Teem-users] unu join segmentation fault
>> To: Anastasia Mironova <mironova@...>
>> Cc: teem-users@...
>> Message-ID: <E05E23F2-14FC-4DC6-A86F-0202C69AD955@...>
>> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>>
>> Hello-
>>
>> Thanks for debugging the issue as much as you did.
>>
>> Can you put the files online?
>>
>> Also, are you using the latest SVN checkout?
>>
>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>
>> Gordon
>>
>> On Aug 11, 2008, at 12:47 PM, Anastasia Mironova wrote:
>>
>>> Hello All,
>>>
>>> I am getting a Segmentation Fault out of
>>>
>>> unu join -i normal0/mean.nrrd normal1/mean.nrrd -a 0 | unu
>>> save -f nrrd -e ascii -i - -o mean.nhdr
>>>
>>> I have tried the following:
>>> - used the unu join command with other files - works
>>> - used unu minmax command on both input files - works
>>> - used more on both input files - works
>>> - saved those files into a different format - doesn't help
>>> - saved those files into a different directory - doesn't
>>> help
>>> - used unu to write a sample test file into the current
>>> directory to test writing issues - works
>>> - space is not an issue - there's 53 GB available...
>>> - tried running it on different machines and as different
>>> users - doesnt' work either
>>>
>>> PLEASE HELP!...
>>>
>>> Thanks so much!
>>> -Anastasia
>>>
>>>
>>> ---
>>> -------------------------------------------------------------------
>>> ---
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> teem-users mailing list
>>> teem-users@...
>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 11 Aug 2008 19:50:10 -0700
>> From: Daniel Ennis <dbe@...>
>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>> To: teem-users@...
>> Cc: Daniel Ennis <dbe@...>
>> Message-ID: <823F61C6-9F5E-47AB-8A11-D12E170132D1@...>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having  
>> trouble
>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think  
>> there
>> is a problem with the darwin.mk file.  Any thoughts or obvious
>> mistakes in the following?  I started out with:
>>
>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>
>> Into /Users/dbe/bin/
>>
>> Then...
>>
>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>> that reads:
>>
>> TEEM_ENDIAN = 4321
>>
>> to
>>
>> TEEM_ENDIAN = 1234
>>
>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>> Apple), which stuffs everything into /opt/local/
>>
>>   http://www.macports.org/install.php
>>
>>   -OR-
>>
>>   http://guide.macports.org/
>>
>>
>> C) Installed zlib support (http://zlib.darwinports.com/)
>>
>>   i) sudo port install zlib
>>
>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>
>>   i) sudo port install bzip2
>>
>> E) Installed libpng support (http://libpng.darwinports.com/)
>>
>>   i) sudo port install libpng
>>
>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>> but TEEM won't know where to find it unless you do this...
>>
>>   export TEEM_ZLIB_IPATH=-I/opt/local/include
>>   export TEEM_BZIP2_IPATH=-I/opt/local/include
>>   export TEEM_PNG_IPATH=-I/opt/local/include
>>
>>   export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>   export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>   export TEEM_PNG_HPATH=-L/opt/local/lib
>>
>> G) Finally,
>>
>>   cd /Users/dbe/bin/teem/src/
>>   export TEEM_ZLIB
>>   export TEEM_BZIP2
>>   export TEEM_PNG
>>   export TEEM_ARCH=darwin.64
>>
>>   make clobber; make;
>>
>>   cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>
>> The last step reports:
>>
>> ./nrrdSanity: nrrd sanity check passed.
>>
>> ./nrrdSanity: encodings supported in this build:
>> raw: yes
>> ascii: yes
>> hex: yes
>> gz: not available
>> bz2: not available
>> ./nrrdSanity: formats supported in this build:
>> nrrd: yes
>> pnm: yes
>> png: not available
>> vtk: yes
>> text: yes
>> eps: yes
>>
>>
>> Thanks!
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 11 Aug 2008 20:00:49 -0700
>> From: "Amit Chourasia" <amit@...>
>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>> To: "Daniel Ennis" <dbe@...>,
>>   <teem-users@...>
>> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2948@...>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Daniel,
>>
>> Add the following before running make and see if it works
>>
>> export TEEM_EXT=1
>> export TEEM_PNG=1
>> export TEEM_ZLIB=1
>>
>> --Amit
>>
>>
>> -----Original Message-----
>> From: teem-users-bounces@... on behalf of Daniel
>> Ennis
>> Sent: Mon 8/11/2008 7:50 PM
>> To: teem-users@...
>> Cc: Daniel Ennis
>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>
>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having  
>> trouble
>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think  
>> there
>> is a problem with the darwin.mk file.  Any thoughts or obvious
>> mistakes in the following?  I started out with:
>>
>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>
>> Into /Users/dbe/bin/
>>
>> Then...
>>
>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>> that reads:
>>
>> TEEM_ENDIAN = 4321
>>
>> to
>>
>> TEEM_ENDIAN = 1234
>>
>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>> Apple), which stuffs everything into /opt/local/
>>
>>   http://www.macports.org/install.php
>>
>>   -OR-
>>
>>   http://guide.macports.org/
>>
>>
>> C) Installed zlib support (http://zlib.darwinports.com/)
>>
>>   i) sudo port install zlib
>>
>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>
>>   i) sudo port install bzip2
>>
>> E) Installed libpng support (http://libpng.darwinports.com/)
>>
>>   i) sudo port install libpng
>>
>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>> but TEEM won't know where to find it unless you do this...
>>
>>   export TEEM_ZLIB_IPATH=-I/opt/local/include
>>   export TEEM_BZIP2_IPATH=-I/opt/local/include
>>   export TEEM_PNG_IPATH=-I/opt/local/include
>>
>>   export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>   export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>   export TEEM_PNG_HPATH=-L/opt/local/lib
>>
>> G) Finally,
>>
>>   cd /Users/dbe/bin/teem/src/
>>   export TEEM_ZLIB
>>   export TEEM_BZIP2
>>   export TEEM_PNG
>>   export TEEM_ARCH=darwin.64
>>
>>   make clobber; make;
>>
>>   cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>
>> The last step reports:
>>
>> ./nrrdSanity: nrrd sanity check passed.
>>
>> ./nrrdSanity: encodings supported in this build:
>> raw: yes
>> ascii: yes
>> hex: yes
>> gz: not available
>> bz2: not available
>> ./nrrdSanity: formats supported in this build:
>> nrrd: yes
>> pnm: yes
>> png: not available
>> vtk: yes
>> text: yes
>> eps: yes
>>
>>
>> Thanks!
>>
>> ---
>> ----------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 11 Aug 2008 20:04:07 -0700
>> From: "Amit Chourasia" <amit@...>
>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>> To: "Daniel Ennis" <dbe@...>,
>>   <teem-users@...>
>> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2949@...>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Also, make sure all the dependent libraries(zlib, png, bzip2) are
>> built in 64 bit.
>>
>>
>>
>> -----Original Message-----
>> From: teem-users-bounces@... on behalf of Daniel
>> Ennis
>> Sent: Mon 8/11/2008 7:50 PM
>> To: teem-users@...
>> Cc: Daniel Ennis
>> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>>
>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having  
>> trouble
>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think  
>> there
>> is a problem with the darwin.mk file.  Any thoughts or obvious
>> mistakes in the following?  I started out with:
>>
>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>
>> Into /Users/dbe/bin/
>>
>> Then...
>>
>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>> that reads:
>>
>> TEEM_ENDIAN = 4321
>>
>> to
>>
>> TEEM_ENDIAN = 1234
>>
>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>> Apple), which stuffs everything into /opt/local/
>>
>>   http://www.macports.org/install.php
>>
>>   -OR-
>>
>>   http://guide.macports.org/
>>
>>
>> C) Installed zlib support (http://zlib.darwinports.com/)
>>
>>   i) sudo port install zlib
>>
>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>
>>   i) sudo port install bzip2
>>
>> E) Installed libpng support (http://libpng.darwinports.com/)
>>
>>   i) sudo port install libpng
>>
>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>> but TEEM won't know where to find it unless you do this...
>>
>>   export TEEM_ZLIB_IPATH=-I/opt/local/include
>>   export TEEM_BZIP2_IPATH=-I/opt/local/include
>>   export TEEM_PNG_IPATH=-I/opt/local/include
>>
>>   export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>   export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>   export TEEM_PNG_HPATH=-L/opt/local/lib
>>
>> G) Finally,
>>
>>   cd /Users/dbe/bin/teem/src/
>>   export TEEM_ZLIB
>>   export TEEM_BZIP2
>>   export TEEM_PNG
>>   export TEEM_ARCH=darwin.64
>>
>>   make clobber; make;
>>
>>   cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>
>> The last step reports:
>>
>> ./nrrdSanity: nrrd sanity check passed.
>>
>> ./nrrdSanity: encodings supported in this build:
>> raw: yes
>> ascii: yes
>> hex: yes
>> gz: not available
>> bz2: not available
>> ./nrrdSanity: formats supported in this build:
>> nrrd: yes
>> pnm: yes
>> png: not available
>> vtk: yes
>> text: yes
>> eps: yes
>>
>>
>> Thanks!
>>
>> ---
>> ----------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Mon, 11 Aug 2008 20:15:00 -0700
>> From: Xavier Tricoche <tricoche@...>
>> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
>> To: Daniel Ennis <dbe@...>
>> Cc: Daniel Ennis <dbe@...>,
>>   "teem-users@..." <teem- 
>> users@...
>>>
>> Message-ID: <397A9647-CF41-4328-A877-9A0BFF126AE6@...>
>> Content-Type: text/plain;    charset=us-ascii;    format=flowed;
>> delsp=yes
>>
>> Hi,
>>
>> I found CMake to take the pain out of it. Any good reason not to use
>> it?
>>
>> Xavier
>>
>> Sent from my iPhone
>>
>> On Aug 11, 2008, at 7:50 PM, Daniel Ennis <dbe@...> wrote:
>>
>>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having
>>> trouble
>>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think
>>> there
>>> is a problem with the darwin.mk file.  Any thoughts or obvious
>>> mistakes in the following?  I started out with:
>>>
>>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>>
>>> Into /Users/dbe/bin/
>>>
>>> Then...
>>>
>>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>>> that reads:
>>>
>>> TEEM_ENDIAN = 4321
>>>
>>> to
>>>
>>> TEEM_ENDIAN = 1234
>>>
>>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>>> Apple), which stuffs everything into /opt/local/
>>>
>>>  http://www.macports.org/install.php
>>>
>>>  -OR-
>>>
>>>  http://guide.macports.org/
>>>
>>>
>>> C) Installed zlib support (http://zlib.darwinports.com/)
>>>
>>>  i) sudo port install zlib
>>>
>>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>>
>>>  i) sudo port install bzip2
>>>
>>> E) Installed libpng support (http://libpng.darwinports.com/)
>>>
>>>  i) sudo port install libpng
>>>
>>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>>> but TEEM won't know where to find it unless you do this...
>>>
>>>  export TEEM_ZLIB_IPATH=-I/opt/local/include
>>>  export TEEM_BZIP2_IPATH=-I/opt/local/include
>>>  export TEEM_PNG_IPATH=-I/opt/local/include
>>>
>>>  export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>>  export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>>  export TEEM_PNG_HPATH=-L/opt/local/lib
>>>
>>> G) Finally,
>>>
>>>  cd /Users/dbe/bin/teem/src/
>>>  export TEEM_ZLIB
>>>  export TEEM_BZIP2
>>>  export TEEM_PNG
>>>  export TEEM_ARCH=darwin.64
>>>
>>>  make clobber; make;
>>>
>>>  cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>>
>>> The last step reports:
>>>
>>> ./nrrdSanity: nrrd sanity check passed.
>>>
>>> ./nrrdSanity: encodings supported in this build:
>>> raw: yes
>>> ascii: yes
>>> hex: yes
>>> gz: not available
>>> bz2: not available
>>> ./nrrdSanity: formats supported in this build:
>>> nrrd: yes
>>> pnm: yes
>>> png: not available
>>> vtk: yes
>>> text: yes
>>> eps: yes
>>>
>>>
>>> Thanks!
>>>
>>> ---
>>> ---
>>> -------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> teem-users mailing list
>>> teem-users@...
>>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>
>>
>>
>> ------------------------------
>>
>> ---
>> ----------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>
>> ------------------------------
>>
>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>>
>>
>> End of teem-users Digest, Vol 23, Issue 5
>> *****************************************
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> teem-users mailing list
> teem-users@...
> https://lists.sourceforge.net/lists/listinfo/teem-users

Re: [Teem-users] teem-users Digest, Vol 23, Issue 5

[Daniel Ennis <dbe@st...>]

Perhaps my problem, in part, is indicative of documentation issues, my  
own pedestrian abilities, or both.

I'll try the other options when I'm back at my desktop, but can  
someone point me to more info about using Cmake?

--
Daniel Ennis, Ph.D
Assistant Professor
University of California, Los Angeles
David Geffen School of Medicine
Department of Radiological Sciences
Diagnostic Cardiovascular Imaging

On Aug 11, 2008, at 20:15, teem-users-request@...  
wrote:

> Send teem-users mailing list submissions to
>    teem-users@...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>    https://lists.sourceforge.net/lists/listinfo/teem-users
> or, via email, send a message with subject or body 'help' to
>    teem-users-request@...
>
> You can reach the person managing the list at
>    teem-users-owner@...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of teem-users digest..."
>
>
> Today's Topics:
>
>   1. Re: unu join segmentation fault (Gordon Kindlmann)
>   2. Building TEEM (darwin.64 specific?) (Daniel Ennis)
>   3. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>   4. Re: Building TEEM (darwin.64 specific?) (Amit Chourasia)
>   5. Re: Building TEEM (darwin.64 specific?) (Xavier Tricoche)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Aug 2008 17:04:13 -0400
> From: Gordon Kindlmann <gk@...>
> Subject: Re: [Teem-users] unu join segmentation fault
> To: Anastasia Mironova <mironova@...>
> Cc: teem-users@...
> Message-ID: <E05E23F2-14FC-4DC6-A86F-0202C69AD955@...>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Hello-
>
> Thanks for debugging the issue as much as you did.
>
> Can you put the files online?
>
> Also, are you using the latest SVN checkout?
>
> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>
> Gordon
>
> On Aug 11, 2008, at 12:47 PM, Anastasia Mironova wrote:
>
>> Hello All,
>>
>> I am getting a Segmentation Fault out of
>>
>> unu join -i normal0/mean.nrrd normal1/mean.nrrd -a 0 | unu
>> save -f nrrd -e ascii -i - -o mean.nhdr
>>
>> I have tried the following:
>> - used the unu join command with other files - works
>> - used unu minmax command on both input files - works
>> - used more on both input files - works
>> - saved those files into a different format - doesn't help
>> - saved those files into a different directory - doesn't
>> help
>> - used unu to write a sample test file into the current
>> directory to test writing issues - works
>> - space is not an issue - there's 53 GB available...
>> - tried running it on different machines and as different
>> users - doesnt' work either
>>
>> PLEASE HELP!...
>>
>> Thanks so much!
>> -Anastasia
>>
>>
>> --- 
>> -------------------------------------------------------------------
>> ---
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Aug 2008 19:50:10 -0700
> From: Daniel Ennis <dbe@...>
> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
> To: teem-users@...
> Cc: Daniel Ennis <dbe@...>
> Message-ID: <823F61C6-9F5E-47AB-8A11-D12E170132D1@...>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having trouble
> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think there
> is a problem with the darwin.mk file.  Any thoughts or obvious
> mistakes in the following?  I started out with:
>
> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>
> Into /Users/dbe/bin/
>
> Then...
>
> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
> that reads:
>
> TEEM_ENDIAN = 4321
>
> to
>
> TEEM_ENDIAN = 1234
>
> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
> Apple), which stuffs everything into /opt/local/
>
>    http://www.macports.org/install.php
>
>    -OR-
>
>    http://guide.macports.org/
>
>
> C) Installed zlib support (http://zlib.darwinports.com/)
>
>    i) sudo port install zlib
>
> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>
>    i) sudo port install bzip2
>
> E) Installed libpng support (http://libpng.darwinports.com/)
>
>    i) sudo port install libpng
>
> F) All of the Mac Ports stuff is installed in /opt/local/be default,
> but TEEM won't know where to find it unless you do this...
>
>    export TEEM_ZLIB_IPATH=-I/opt/local/include
>    export TEEM_BZIP2_IPATH=-I/opt/local/include
>    export TEEM_PNG_IPATH=-I/opt/local/include
>
>    export TEEM_ZLIB_HPATH=-L/opt/local/lib
>    export TEEM_BZIP2_HPATH=-L/opt/local/lib
>    export TEEM_PNG_HPATH=-L/opt/local/lib
>
> G) Finally,
>
>    cd /Users/dbe/bin/teem/src/
>    export TEEM_ZLIB
>    export TEEM_BZIP2
>    export TEEM_PNG
>    export TEEM_ARCH=darwin.64
>
>    make clobber; make;
>
>    cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>
> The last step reports:
>
> ./nrrdSanity: nrrd sanity check passed.
>
> ./nrrdSanity: encodings supported in this build:
> raw: yes
> ascii: yes
> hex: yes
> gz: not available
> bz2: not available
> ./nrrdSanity: formats supported in this build:
> nrrd: yes
> pnm: yes
> png: not available
> vtk: yes
> text: yes
> eps: yes
>
>
> Thanks!
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 11 Aug 2008 20:00:49 -0700
> From: "Amit Chourasia" <amit@...>
> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
> To: "Daniel Ennis" <dbe@...>,
>    <teem-users@...>
> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2948@...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Daniel,
>
> Add the following before running make and see if it works
>
> export TEEM_EXT=1
> export TEEM_PNG=1
> export TEEM_ZLIB=1
>
> --Amit
>
>
> -----Original Message-----
> From: teem-users-bounces@... on behalf of Daniel  
> Ennis
> Sent: Mon 8/11/2008 7:50 PM
> To: teem-users@...
> Cc: Daniel Ennis
> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>
> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having trouble
> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think there
> is a problem with the darwin.mk file.  Any thoughts or obvious
> mistakes in the following?  I started out with:
>
> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>
> Into /Users/dbe/bin/
>
> Then...
>
> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
> that reads:
>
> TEEM_ENDIAN = 4321
>
> to
>
> TEEM_ENDIAN = 1234
>
> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
> Apple), which stuffs everything into /opt/local/
>
>    http://www.macports.org/install.php
>
>    -OR-
>
>    http://guide.macports.org/
>
>
> C) Installed zlib support (http://zlib.darwinports.com/)
>
>    i) sudo port install zlib
>
> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>
>    i) sudo port install bzip2
>
> E) Installed libpng support (http://libpng.darwinports.com/)
>
>    i) sudo port install libpng
>
> F) All of the Mac Ports stuff is installed in /opt/local/be default,
> but TEEM won't know where to find it unless you do this...
>
>    export TEEM_ZLIB_IPATH=-I/opt/local/include
>    export TEEM_BZIP2_IPATH=-I/opt/local/include
>    export TEEM_PNG_IPATH=-I/opt/local/include
>
>    export TEEM_ZLIB_HPATH=-L/opt/local/lib
>    export TEEM_BZIP2_HPATH=-L/opt/local/lib
>    export TEEM_PNG_HPATH=-L/opt/local/lib
>
> G) Finally,
>
>    cd /Users/dbe/bin/teem/src/
>    export TEEM_ZLIB
>    export TEEM_BZIP2
>    export TEEM_PNG
>    export TEEM_ARCH=darwin.64
>
>    make clobber; make;
>
>    cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>
> The last step reports:
>
> ./nrrdSanity: nrrd sanity check passed.
>
> ./nrrdSanity: encodings supported in this build:
> raw: yes
> ascii: yes
> hex: yes
> gz: not available
> bz2: not available
> ./nrrdSanity: formats supported in this build:
> nrrd: yes
> pnm: yes
> png: not available
> vtk: yes
> text: yes
> eps: yes
>
>
> Thanks!
>
> --- 
> ----------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> teem-users mailing list
> teem-users@...
> https://lists.sourceforge.net/lists/listinfo/teem-users
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 4
> Date: Mon, 11 Aug 2008 20:04:07 -0700
> From: "Amit Chourasia" <amit@...>
> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
> To: "Daniel Ennis" <dbe@...>,
>    <teem-users@...>
> Message-ID: <452F37AE49199D49B1702D7D45038C4D8C2949@...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Also, make sure all the dependent libraries(zlib, png, bzip2) are  
> built in 64 bit.
>
>
>
> -----Original Message-----
> From: teem-users-bounces@... on behalf of Daniel  
> Ennis
> Sent: Mon 8/11/2008 7:50 PM
> To: teem-users@...
> Cc: Daniel Ennis
> Subject: [Teem-users] Building TEEM (darwin.64 specific?)
>
> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having trouble
> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think there
> is a problem with the darwin.mk file.  Any thoughts or obvious
> mistakes in the following?  I started out with:
>
> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>
> Into /Users/dbe/bin/
>
> Then...
>
> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
> that reads:
>
> TEEM_ENDIAN = 4321
>
> to
>
> TEEM_ENDIAN = 1234
>
> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
> Apple), which stuffs everything into /opt/local/
>
>    http://www.macports.org/install.php
>
>    -OR-
>
>    http://guide.macports.org/
>
>
> C) Installed zlib support (http://zlib.darwinports.com/)
>
>    i) sudo port install zlib
>
> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>
>    i) sudo port install bzip2
>
> E) Installed libpng support (http://libpng.darwinports.com/)
>
>    i) sudo port install libpng
>
> F) All of the Mac Ports stuff is installed in /opt/local/be default,
> but TEEM won't know where to find it unless you do this...
>
>    export TEEM_ZLIB_IPATH=-I/opt/local/include
>    export TEEM_BZIP2_IPATH=-I/opt/local/include
>    export TEEM_PNG_IPATH=-I/opt/local/include
>
>    export TEEM_ZLIB_HPATH=-L/opt/local/lib
>    export TEEM_BZIP2_HPATH=-L/opt/local/lib
>    export TEEM_PNG_HPATH=-L/opt/local/lib
>
> G) Finally,
>
>    cd /Users/dbe/bin/teem/src/
>    export TEEM_ZLIB
>    export TEEM_BZIP2
>    export TEEM_PNG
>    export TEEM_ARCH=darwin.64
>
>    make clobber; make;
>
>    cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>
> The last step reports:
>
> ./nrrdSanity: nrrd sanity check passed.
>
> ./nrrdSanity: encodings supported in this build:
> raw: yes
> ascii: yes
> hex: yes
> gz: not available
> bz2: not available
> ./nrrdSanity: formats supported in this build:
> nrrd: yes
> pnm: yes
> png: not available
> vtk: yes
> text: yes
> eps: yes
>
>
> Thanks!
>
> --- 
> ----------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> teem-users mailing list
> teem-users@...
> https://lists.sourceforge.net/lists/listinfo/teem-users
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 5
> Date: Mon, 11 Aug 2008 20:15:00 -0700
> From: Xavier Tricoche <tricoche@...>
> Subject: Re: [Teem-users] Building TEEM (darwin.64 specific?)
> To: Daniel Ennis <dbe@...>
> Cc: Daniel Ennis <dbe@...>,
>    "teem-users@..." <teem-users@... 
> >
> Message-ID: <397A9647-CF41-4328-A877-9A0BFF126AE6@...>
> Content-Type: text/plain;    charset=us-ascii;    format=flowed;     
> delsp=yes
>
> Hi,
>
> I found CMake to take the pain out of it. Any good reason not to use  
> it?
>
> Xavier
>
> Sent from my iPhone
>
> On Aug 11, 2008, at 7:50 PM, Daniel Ennis <dbe@...> wrote:
>
>> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having  
>> trouble
>> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think  
>> there
>> is a problem with the darwin.mk file.  Any thoughts or obvious
>> mistakes in the following?  I started out with:
>>
>> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>>
>> Into /Users/dbe/bin/
>>
>> Then...
>>
>> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
>> that reads:
>>
>> TEEM_ENDIAN = 4321
>>
>> to
>>
>> TEEM_ENDIAN = 1234
>>
>> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
>> Apple), which stuffs everything into /opt/local/
>>
>>   http://www.macports.org/install.php
>>
>>   -OR-
>>
>>   http://guide.macports.org/
>>
>>
>> C) Installed zlib support (http://zlib.darwinports.com/)
>>
>>   i) sudo port install zlib
>>
>> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>>
>>   i) sudo port install bzip2
>>
>> E) Installed libpng support (http://libpng.darwinports.com/)
>>
>>   i) sudo port install libpng
>>
>> F) All of the Mac Ports stuff is installed in /opt/local/be default,
>> but TEEM won't know where to find it unless you do this...
>>
>>   export TEEM_ZLIB_IPATH=-I/opt/local/include
>>   export TEEM_BZIP2_IPATH=-I/opt/local/include
>>   export TEEM_PNG_IPATH=-I/opt/local/include
>>
>>   export TEEM_ZLIB_HPATH=-L/opt/local/lib
>>   export TEEM_BZIP2_HPATH=-L/opt/local/lib
>>   export TEEM_PNG_HPATH=-L/opt/local/lib
>>
>> G) Finally,
>>
>>   cd /Users/dbe/bin/teem/src/
>>   export TEEM_ZLIB
>>   export TEEM_BZIP2
>>   export TEEM_PNG
>>   export TEEM_ARCH=darwin.64
>>
>>   make clobber; make;
>>
>>   cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>>
>> The last step reports:
>>
>> ./nrrdSanity: nrrd sanity check passed.
>>
>> ./nrrdSanity: encodings supported in this build:
>> raw: yes
>> ascii: yes
>> hex: yes
>> gz: not available
>> bz2: not available
>> ./nrrdSanity: formats supported in this build:
>> nrrd: yes
>> pnm: yes
>> png: not available
>> vtk: yes
>> text: yes
>> eps: yes
>>
>>
>> Thanks!
>>
>> ---
>> --- 
>> -------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>
>
>
> ------------------------------
>
> --- 
> ----------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>
> ------------------------------
>
> _______________________________________________
> teem-users mailing list
> teem-users@...
> https://lists.sourceforge.net/lists/listinfo/teem-users
>
>
> End of teem-users Digest, Vol 23, Issue 5
> *****************************************

Re: [Teem-users] Building TEEM (darwin.64 specific?)

[Xavier Tricoche <tricoche@sc...>]

Hi,

I found CMake to take the pain out of it. Any good reason not to use it?

Xavier

Sent from my iPhone

On Aug 11, 2008, at 7:50 PM, Daniel Ennis <dbe@...> wrote:

> Hi - I'm trying to get TEEM built on my Mac Pro and I'm having trouble
> getting the ZLIB, BZIP2, and PNG support to work.  Also, I think there
> is a problem with the darwin.mk file.  Any thoughts or obvious
> mistakes in the following?  I started out with:
>
> svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem
>
> Into /Users/dbe/bin/
>
> Then...
>
> A) For 64-bit edit .../teem/src/make/darwin.mk and change the line
> that reads:
>
> TEEM_ENDIAN = 4321
>
> to
>
> TEEM_ENDIAN = 1234
>
> B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from
> Apple), which stuffs everything into /opt/local/
>
>    http://www.macports.org/install.php
>
>    -OR-
>
>    http://guide.macports.org/
>
>
> C) Installed zlib support (http://zlib.darwinports.com/)
>
>    i) sudo port install zlib
>
> D) Installed bzip2 support (http://bzip2.darwinports.com/)
>
>    i) sudo port install bzip2
>
> E) Installed libpng support (http://libpng.darwinports.com/)
>
>    i) sudo port install libpng
>
> F) All of the Mac Ports stuff is installed in /opt/local/be default,
> but TEEM won't know where to find it unless you do this...
>
>    export TEEM_ZLIB_IPATH=-I/opt/local/include
>    export TEEM_BZIP2_IPATH=-I/opt/local/include
>    export TEEM_PNG_IPATH=-I/opt/local/include
>
>    export TEEM_ZLIB_HPATH=-L/opt/local/lib
>    export TEEM_BZIP2_HPATH=-L/opt/local/lib
>    export TEEM_PNG_HPATH=-L/opt/local/lib
>
> G) Finally,
>
>    cd /Users/dbe/bin/teem/src/
>    export TEEM_ZLIB
>    export TEEM_BZIP2
>    export TEEM_PNG
>    export TEEM_ARCH=darwin.64
>
>    make clobber; make;
>
>    cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity
>
> The last step reports:
>
> ./nrrdSanity: nrrd sanity check passed.
>
> ./nrrdSanity: encodings supported in this build:
> raw: yes
> ascii: yes
> hex: yes
> gz: not available
> bz2: not available
> ./nrrdSanity: formats supported in this build:
> nrrd: yes
> pnm: yes
> png: not available
> vtk: yes
> text: yes
> eps: yes
>
>
> Thanks!
>
> ---
> ----------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> teem-users mailing list
> teem-users@...
> https://lists.sourceforge.net/lists/listinfo/teem-users

Re: [Teem-users] Building TEEM (darwin.64 specific?)

[Amit Chourasia <amit@sd...>]

Also, make sure all the dependent libraries(zlib, png, bzip2) are built in 64 bit.



-----Original Message-----
From: teem-users-bounces@... on behalf of Daniel Ennis
Sent: Mon 8/11/2008 7:50 PM
To: teem-users@...
Cc: Daniel Ennis
Subject: [Teem-users] Building TEEM (darwin.64 specific?)
 
Hi - I'm trying to get TEEM built on my Mac Pro and I'm having trouble  
getting the ZLIB, BZIP2, and PNG support to work.  Also, I think there  
is a problem with the darwin.mk file.  Any thoughts or obvious  
mistakes in the following?  I started out with:

svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem

Into /Users/dbe/bin/

Then...

A) For 64-bit edit .../teem/src/make/darwin.mk and change the line  
that reads:

TEEM_ENDIAN = 4321

to

TEEM_ENDIAN = 1234

B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from  
Apple), which stuffs everything into /opt/local/

	http://www.macports.org/install.php

	-OR-

	http://guide.macports.org/


C) Installed zlib support (http://zlib.darwinports.com/)

	i) sudo port install zlib

D) Installed bzip2 support (http://bzip2.darwinports.com/)

	i) sudo port install bzip2

E) Installed libpng support (http://libpng.darwinports.com/)
	
	i) sudo port install libpng

F) All of the Mac Ports stuff is installed in /opt/local/be default,  
but TEEM won't know where to find it unless you do this...
	
	export TEEM_ZLIB_IPATH=-I/opt/local/include
	export TEEM_BZIP2_IPATH=-I/opt/local/include
	export TEEM_PNG_IPATH=-I/opt/local/include
	
	export TEEM_ZLIB_HPATH=-L/opt/local/lib
	export TEEM_BZIP2_HPATH=-L/opt/local/lib
	export TEEM_PNG_HPATH=-L/opt/local/lib
	
G) Finally,

	cd /Users/dbe/bin/teem/src/
	export TEEM_ZLIB
	export TEEM_BZIP2
	export TEEM_PNG
	export TEEM_ARCH=darwin.64

	make clobber; make;

	cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity

The last step reports:

./nrrdSanity: nrrd sanity check passed.

./nrrdSanity: encodings supported in this build:
raw: yes
ascii: yes
hex: yes
gz: not available
bz2: not available
./nrrdSanity: formats supported in this build:
nrrd: yes
pnm: yes
png: not available
vtk: yes
text: yes
eps: yes


Thanks!

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Re: [Teem-users] Building TEEM (darwin.64 specific?)

[Amit Chourasia <amit@sd...>]

Daniel,

Add the following before running make and see if it works

export TEEM_EXT=1
export TEEM_PNG=1
export TEEM_ZLIB=1

--Amit


-----Original Message-----
From: teem-users-bounces@... on behalf of Daniel Ennis
Sent: Mon 8/11/2008 7:50 PM
To: teem-users@...
Cc: Daniel Ennis
Subject: [Teem-users] Building TEEM (darwin.64 specific?)
 
Hi - I'm trying to get TEEM built on my Mac Pro and I'm having trouble  
getting the ZLIB, BZIP2, and PNG support to work.  Also, I think there  
is a problem with the darwin.mk file.  Any thoughts or obvious  
mistakes in the following?  I started out with:

svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem

Into /Users/dbe/bin/

Then...

A) For 64-bit edit .../teem/src/make/darwin.mk and change the line  
that reads:

TEEM_ENDIAN = 4321

to

TEEM_ENDIAN = 1234

B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from  
Apple), which stuffs everything into /opt/local/

	http://www.macports.org/install.php

	-OR-

	http://guide.macports.org/


C) Installed zlib support (http://zlib.darwinports.com/)

	i) sudo port install zlib

D) Installed bzip2 support (http://bzip2.darwinports.com/)

	i) sudo port install bzip2

E) Installed libpng support (http://libpng.darwinports.com/)
	
	i) sudo port install libpng

F) All of the Mac Ports stuff is installed in /opt/local/be default,  
but TEEM won't know where to find it unless you do this...
	
	export TEEM_ZLIB_IPATH=-I/opt/local/include
	export TEEM_BZIP2_IPATH=-I/opt/local/include
	export TEEM_PNG_IPATH=-I/opt/local/include
	
	export TEEM_ZLIB_HPATH=-L/opt/local/lib
	export TEEM_BZIP2_HPATH=-L/opt/local/lib
	export TEEM_PNG_HPATH=-L/opt/local/lib
	
G) Finally,

	cd /Users/dbe/bin/teem/src/
	export TEEM_ZLIB
	export TEEM_BZIP2
	export TEEM_PNG
	export TEEM_ARCH=darwin.64

	make clobber; make;

	cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity

The last step reports:

./nrrdSanity: nrrd sanity check passed.

./nrrdSanity: encodings supported in this build:
raw: yes
ascii: yes
hex: yes
gz: not available
bz2: not available
./nrrdSanity: formats supported in this build:
nrrd: yes
pnm: yes
png: not available
vtk: yes
text: yes
eps: yes


Thanks!

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[Teem-users] Building TEEM (darwin.64 specific?)

[Daniel Ennis <dbe@st...>]

Hi - I'm trying to get TEEM built on my Mac Pro and I'm having trouble  
getting the ZLIB, BZIP2, and PNG support to work.  Also, I think there  
is a problem with the darwin.mk file.  Any thoughts or obvious  
mistakes in the following?  I started out with:

svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem

Into /Users/dbe/bin/

Then...

A) For 64-bit edit .../teem/src/make/darwin.mk and change the line  
that reads:

TEEM_ENDIAN = 4321

to

TEEM_ENDIAN = 1234

B) Installed MacPorts (Requires XCode, X11 and X11 SDK all from  
Apple), which stuffs everything into /opt/local/

	http://www.macports.org/install.php

	-OR-

	http://guide.macports.org/


C) Installed zlib support (http://zlib.darwinports.com/)

	i) sudo port install zlib

D) Installed bzip2 support (http://bzip2.darwinports.com/)

	i) sudo port install bzip2

E) Installed libpng support (http://libpng.darwinports.com/)
	
	i) sudo port install libpng

F) All of the Mac Ports stuff is installed in /opt/local/be default,  
but TEEM won't know where to find it unless you do this...
	
	export TEEM_ZLIB_IPATH=-I/opt/local/include
	export TEEM_BZIP2_IPATH=-I/opt/local/include
	export TEEM_PNG_IPATH=-I/opt/local/include
	
	export TEEM_ZLIB_HPATH=-L/opt/local/lib
	export TEEM_BZIP2_HPATH=-L/opt/local/lib
	export TEEM_PNG_HPATH=-L/opt/local/lib
	
G) Finally,

	cd /Users/dbe/bin/teem/src/
	export TEEM_ZLIB
	export TEEM_BZIP2
	export TEEM_PNG
	export TEEM_ARCH=darwin.64

	make clobber; make;

	cd /Users/dbe/bin/teem/darwin.64/bin/; ./nrrdSanity

The last step reports:

./nrrdSanity: nrrd sanity check passed.

./nrrdSanity: encodings supported in this build:
raw: yes
ascii: yes
hex: yes
gz: not available
bz2: not available
./nrrdSanity: formats supported in this build:
nrrd: yes
pnm: yes
png: not available
vtk: yes
text: yes
eps: yes


Thanks!

Re: [Teem-users] unu join segmentation fault

[Gordon Kindlmann <gk@bw...>]

Hello-

Thanks for debugging the issue as much as you did.

Can you put the files online?

Also, are you using the latest SVN checkout?

svn co https://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem

Gordon

On Aug 11, 2008, at 12:47 PM, Anastasia Mironova wrote:

> Hello All,
>
> I am getting a Segmentation Fault out of
>
> unu join -i normal0/mean.nrrd normal1/mean.nrrd -a 0 | unu
> save -f nrrd -e ascii -i - -o mean.nhdr
>
> I have tried the following:
> - used the unu join command with other files - works
> - used unu minmax command on both input files - works
> - used more on both input files - works
> - saved those files into a different format - doesn't help
> - saved those files into a different directory - doesn't
> help
> - used unu to write a sample test file into the current
> directory to test writing issues - works
> - space is not an issue - there's 53 GB available...
> - tried running it on different machines and as different
> users - doesnt' work either
>
> PLEASE HELP!...
>
> Thanks so much!
> -Anastasia
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.Net email is sponsored by the Moblin Your Move Developer's  
> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
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> the world
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[Teem-users] unu join segmentation fault

[Anastasia Mironova <mironova@sc...>]

Hello All,

I am getting a Segmentation Fault out of

unu join -i normal0/mean.nrrd normal1/mean.nrrd -a 0 | unu 
save -f nrrd -e ascii -i - -o mean.nhdr

I have tried the following:
- used the unu join command with other files - works
- used unu minmax command on both input files - works
- used more on both input files - works
- saved those files into a different format - doesn't help
- saved those files into a different directory - doesn't 
help
- used unu to write a sample test file into the current 
directory to test writing issues - works
- space is not an issue - there's 53 GB available...
- tried running it on different machines and as different 
users - doesnt' work either

PLEASE HELP!...

Thanks so much!
-Anastasia

Re: [Teem-users] Heightmap to nrrd

[Jonas Forsslund <jonas@fo...>]

Thats great!
I appreciate the example commands too, starting to learn the
flexibility of using teem and this is very neat. I had to quantize it
as well to render it by my marching cubes but it worked well.
Also thanks to  the fast respons I got from Jorik.

Thanks
Jonas

2008/8/4 Gordon Kindlmann <gk@...>:
> Hi-
>
> Interesting question.
>
> The basic idea is to exploit the fact that arithmetic operations on nrrds
> will recycle through the arrays values if the operation needs more values
> than are in the array, and, that the size of the output is determined by the
> first array argument.
>
> So if your 8-bit image is in img.png, then you can:
>
>  unu 2op x img.png 0 -o 0.png
>  unu 1op exists -i img.png -o 1.png
>
> which just makes two images of the same size, only with values 0 and 1.
>  Then
>
>  unu join -i 0.png 1.png -a 2 \
>   | unu resample -s = = 200 -k tent -c node -t float \
>   | unu axinfo -a 0 -c node \
>   | unu axinfo -a 1 -c node -o ramps.nrrd
>
> will make a volume of the same X and Y dimensions, which is composed of
> linear ramps from 0 to 1 along the Z axis.  The "-s" arguments to "unu
> resample" are "= = 200", which means its 200 samples along Z, but you can
> change this.  Then
>
>  unu 2op / img.png 255 -t float \
>   | unu 2op / - 3 \
>   | unu 2op + ramps.nrrd - -o vol.nrrd
>
> does the following:
> * 1st "unu 2op" takes the 8-bit image and converts it to a float image
> (values from 0 to 1)
> * 2nd "unu 2op" further reduces values from 0 to 0.33 (just for fun)
> * 3rd "unu 2op" adds the image values to the volume of ramps.  This is the
> important step, and note that the volume "ramps.nrrd" is the first argument
> to "unu 2op", and the image is the second.  unu 2op recycles the image
> values for each Z sample of the volume.
>
> The output "vol.nrrd" has linear ramps along Z, but the values are shifted
> so that the isosurfaces of the volume will be heightfields corresponding to
> the original image.  You can binarize this with "unu 2op gt", or just
> isosurface it as is.  Attached is an image I made for testing, and a surface
> rendering of the heightmap.
>
> thanks for the interesting question,
> Gordon
>
>
> On Aug 4, 2008, at 8:16 AM, Jonas Forsslund wrote:
>
>> Hello,
>>
>> I want to create a raw 3d voxel model (for example 256x256x256) based
>> on a 2d heightmap (a 8 bit 256x256 grayscale bitmap).
>> While I'm new to the more adavanced useage of teem, my guess is that
>> this could be done quite easily in a script or similar using teem
>> (instead of writing a new tool).
>>
>> Any suggestions?
>>
>> Thanks a lot
>> Jonas
>>
>> -------------------------------------------------------------------------
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>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
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>> _______________________________________________
>> teem-users mailing list
>> teem-users@...
>> https://lists.sourceforge.net/lists/listinfo/teem-users
>
>
>

Re: [Teem-users] read only header info

[Gordon Kindlmann <gk@bw...>]

hi-

awesome!  The question goes to teem-users, and someone besides me  
answers first!

Gordon

On Aug 4, 2008, at 6:57 PM, Michael Callahan wrote:

> There is an example on the teem/nrrd website documentation for doing
> this.  It looks vaguely like this:
>
>       NrrdIoState *nio = nrrdIoStateNew();
>       nrrdIoStateSet(nio, nrrdIoStateSkipData, AIR_TRUE);
>       nrrdLoad(nrrd, filename, nio);
>       // Stuff
>       nrrdIoStateNix(nio);
>
>   Michael
>
> On Mon, 2008-08-04 at 12:13 -1000, McKay Davis wrote:
>> Gordon,
>>
>> Is there a way (or function) to parse the -only- the nrrd header from
>> a file and return a Nrrd struct with a NULL data ptr?  I'd like to  
>> get
>> some info from the Nrrd before proceeding with an expensive data  
>> load.
>>
>> Thanks,
>>
>> -McKay Davis
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.Net email is sponsored by the Moblin Your Move Developer's  
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win  
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in  
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________ teem-users mailing  
>> list teem-users@... https:// 
>> lists.sourceforge.net/lists/listinfo/teem-users
>
>
> ---------------------------------------------------------------------- 
> ---
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> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
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> the world
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Re: [Teem-users] read only header info

[Michael Callahan <callahan@sc...>]

There is an example on the teem/nrrd website documentation for doing
this.  It looks vaguely like this:

      NrrdIoState *nio = nrrdIoStateNew();
      nrrdIoStateSet(nio, nrrdIoStateSkipData, AIR_TRUE);
      nrrdLoad(nrrd, filename, nio);
      // Stuff
      nrrdIoStateNix(nio);

  Michael

On Mon, 2008-08-04 at 12:13 -1000, McKay Davis wrote:
> Gordon,
> 
> Is there a way (or function) to parse the -only- the nrrd header from
> a file and return a Nrrd struct with a NULL data ptr?  I'd like to get
> some info from the Nrrd before proceeding with an expensive data load.
> 
> Thanks,
> 
> -McKay Davis
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________ teem-users mailing list teem-users@... https://lists.sourceforge.net/lists/listinfo/teem-users

[Teem-users] read only header info

[McKay Davis <mckay.cpp@gm...>]

Gordon,

Is there a way (or function) to parse the -only- the nrrd header from a file
and return a Nrrd struct with a NULL data ptr?  I'd like to get some info
from the Nrrd before proceeding with an expensive data load.

Thanks,

-McKay Davis

Re: [Teem-users] nrrdStringRead?

[Gordon Kindlmann <gk@bw...>]

hi-

That is the function for "reading" a nrrd from a string that contains  
the header.  I believe it only works for detached headers (data has  
to be in separate file), so there is no general purpose way of  
reading a complete nrrd from memory, sadly.

Because only the header is presumed to be in the string, and because  
the header is ASCII, the 0-termination of the string is used as the  
mark of the end of the string, and no length parameter is required.

Can you post an example of a case where the string buffer is  
overrun?  That is worrisome, but I'm not surprised if there's a bug-  
that funcionalitiy was written in a hurry.

Gordon

On Jul 31, 2008, at 12:42 PM, Michael Callahan wrote:

> I'm not sure how to use nrrdStringRead in a safe manner.  It takes  
> in a
> nrrd pointer, a string buffer, and a Nio pointer.  However it doesn't
> take in a buffer size parameter and appears to overrun the string  
> buffer
> on occasion.
>
> In general how do I read a nrrd out of memory rather than out of a  
> file?
>
>   Michael
>
>
>
> ---------------------------------------------------------------------- 
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> challenge
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> great prizes
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