slicer 3.4 trouble starting

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slicer 3.4 trouble starting

Dianne Patterson
I tarred up my old Slicer dir (version 3.2) and untarred the new Slicer (3.4.2-2010-01-06-darwin-x86.tar.gz)
I'm on Mac OSX Leopard on an Intel Mac Pro.

When I try to start slicer, it goes down into the bin and grabs Slicer3-real, which apparently it cannot start.
If I force it to grab Slicer3 from the main Slicer directory, it will start, but this feels like a hack..
I don't see any mention of the issue online, so I wanted to let you know.

[seth:/usr/local 275] % Slicer3
dyld: Library not loaded: /Users/hayes/Slicer-3-4/Slicer3-lib/teem-build/bin/libteem.1.dylib
  Referenced from: /usr/local/Slicer/bin/Slicer3-real
  Reason: image not found
Trace/BPT trap
--------

Thankyou,

Dianne


--
Dianne Patterson, Ph.D.
[hidden email]
University of Arizona
SLHS 328
621-5105

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Re: slicer 3.4 trouble starting

Dominik Meier
Hi Dianne

I've had similar issues, there are some quirks with the Mac Unix environment that may need tweaking, depending on architecture and OS.

I've added the DYLD library path line below to by .bashrc file to be able to launch 3.5 on my PowerMac:

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/Applications/Slicer3-3.5a/lib/InsightToolkit:/Applications/Slicer
3-3.5a/lib/MRML/:/Applications/Slicer3-3.5a/lib/vtkITK:/Applications/Slicer3-3.5a/lib/vtk-5.4:/Applications/Sl
icer3-3.5a/lib/FreeSurfer:/Applications/Slicer3-3.5a/lib/libvtkTeem.dylib:/Applications/Slicer3-3.5a/lib/vtkTe
em:/Applications/Slicer3-3.5a/lib/Teem-1.10.0

Also you may have to launch X11 first before starting slicer, as it sets different environment variables than "terminal".


______________________________________________
DOMINIK MEIER, PH.D.
Assistant Professor of Radiology, Harvard Medical School
Center for Neurological Imaging, Brigham & Women's Hospital
221 Longwood Avenue, RF396, Boston, MA 02115
Phone: 617 278-0800
Fax: 617 264-5154



On Jan 18, 2010, at 7:47 PM, Dianne Patterson wrote:

I tarred up my old Slicer dir (version 3.2) and untarred the new Slicer (3.4.2-2010-01-06-darwin-x86.tar.gz)
I'm on Mac OSX Leopard on an Intel Mac Pro.

When I try to start slicer, it goes down into the bin and grabs Slicer3-real, which apparently it cannot start.
If I force it to grab Slicer3 from the main Slicer directory, it will start, but this feels like a hack..
I don't see any mention of the issue online, so I wanted to let you know.

[seth:/usr/local 275] % Slicer3
dyld: Library not loaded: /Users/hayes/Slicer-3-4/Slicer3-lib/teem-build/bin/libteem.1.dylib
  Referenced from: /usr/local/Slicer/bin/Slicer3-real
  Reason: image not found
Trace/BPT trap
--------

Thankyou,

Dianne


--
Dianne Patterson, Ph.D.
[hidden email]
University of Arizona
SLHS 328
621-5105
_______________________________________________
slicer-users mailing list
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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Re: slicer 3.4 trouble starting

Curtis Lisle
Hi Dianne!
Have you had a chance to run the setup script to try and fix the DYLD_LIBRARY_PATH dynamically?  I am on a Mac, and I usually have success doing the following:

% cd <slicer-directory>/Slicer3-build/bin
% source ./Slicer3Setup.sh
% ./Slicer3-real

The setup script figures out where the Slicer directory is and fixes the shell variables accordingly.  You can get a look at what the script is doing if you use the command "printenv" before and after running the script.    Once you run the script, Slicer3 can be launched from that shell only.  If you open a new terminal, you will need to re-execute the shell script in the new terminal to run slicer from the new terminal.  This has worked for me reliably on Tiger, Leopard, and Snow Leopard.  

Curtis Lisle



On Jan 19, 2010, at 10:07 AM, Dominik Meier wrote:

Hi Dianne

I've had similar issues, there are some quirks with the Mac Unix environment that may need tweaking, depending on architecture and OS.

I've added the DYLD library path line below to by .bashrc file to be able to launch 3.5 on my PowerMac:

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/Applications/Slicer3-3.5a/lib/InsightToolkit:/Applications/Slicer
3-3.5a/lib/MRML/:/Applications/Slicer3-3.5a/lib/vtkITK:/Applications/Slicer3-3.5a/lib/vtk-5.4:/Applications/Sl
icer3-3.5a/lib/FreeSurfer:/Applications/Slicer3-3.5a/lib/libvtkTeem.dylib:/Applications/Slicer3-3.5a/lib/vtkTe
em:/Applications/Slicer3-3.5a/lib/Teem-1.10.0

Also you may have to launch X11 first before starting slicer, as it sets different environment variables than "terminal".


______________________________________________
DOMINIK MEIER, PH.D.
Assistant Professor of Radiology, Harvard Medical School
Center for Neurological Imaging, Brigham & Women's Hospital
221 Longwood Avenue, RF396, Boston, MA 02115
Phone: 617 278-0800
Fax: 617 264-5154



On Jan 18, 2010, at 7:47 PM, Dianne Patterson wrote:

I tarred up my old Slicer dir (version 3.2) and untarred the new Slicer (3.4.2-2010-01-06-darwin-x86.tar.gz)
I'm on Mac OSX Leopard on an Intel Mac Pro.

When I try to start slicer, it goes down into the bin and grabs Slicer3-real, which apparently it cannot start.
If I force it to grab Slicer3 from the main Slicer directory, it will start, but this feels like a hack..
I don't see any mention of the issue online, so I wanted to let you know.

[seth:/usr/local 275] % Slicer3
dyld: Library not loaded: /Users/hayes/Slicer-3-4/Slicer3-lib/teem-build/bin/libteem.1.dylib
  Referenced from: /usr/local/Slicer/bin/Slicer3-real
  Reason: image not found
Trace/BPT trap
--------

Thankyou,

Dianne


--
Dianne Patterson, Ph.D.
[hidden email]
University of Arizona
SLHS 328
621-5105
_______________________________________________
slicer-users mailing list
To unsubscribe: send email to [hidden email] with unsubscribe as the subject

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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Re: slicer 3.4 trouble starting

pieper
Administrator
Hi Folks -

Here's another suggestion - be sure to type ./Slicer3 when launching the
executable (to be sure you are getting the one from the local
directory).  This will invoke the launcher program that will figure out
the correct paths for you before starting bin/Slicer3-real.  With this
method, you shouldn't have to change your DYLD_LIBRARY_PATH and you can
have multiple versions of slicer installed on your machine in case you
need to switch back and forth.

common:Slicer3-3.4.2-2010-01-06-darwin-x86 pieper$ ./Slicer3

Note this should also work if you doubleclick the Slicer3 executable at
the top level of the untarred distribution.

HTH,
Steve

On J/19/10 10:36 AM, Curtis Lisle wrote:

> Hi Dianne!
> Have you had a chance to run the setup script to try and fix the
> DYLD_LIBRARY_PATH dynamically? I am on a Mac, and I usually have success
> doing the following:
>
> % cd <slicer-directory>/Slicer3-build/bin
> % source ./Slicer3Setup.sh
> % ./Slicer3-real
>
> The setup script figures out where the Slicer directory is and fixes the
> shell variables accordingly. You can get a look at what the script is
> doing if you use the command "printenv" before and after running the
> script. Once you run the script, Slicer3 can be launched from that shell
> only. If you open a new terminal, you will need to re-execute the shell
> script in the new terminal to run slicer from the new terminal. This has
> worked for me reliably on Tiger, Leopard, and Snow Leopard.
>
> Curtis Lisle
> [hidden email] <mailto:[hidden email]>
>
>
>
> On Jan 19, 2010, at 10:07 AM, Dominik Meier wrote:
>
>> Hi Dianne
>>
>> I've had similar issues, there are some quirks with the Mac Unix
>> environment that may need tweaking, depending on architecture and OS.
>>
>> I've added the DYLD library path line below to by .bashrc file to be
>> able to launch 3.5 on my PowerMac:
>>
>> export
>> DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/Applications/Slicer3-3.5a/lib/InsightToolkit:/Applications/Slicer
>> 3-3.5a/lib/MRML/:/Applications/Slicer3-3.5a/lib/vtkITK:/Applications/Slicer3-3.5a/lib/vtk-5.4:/Applications/Sl
>> icer3-3.5a/lib/FreeSurfer:/Applications/Slicer3-3.5a/lib/libvtkTeem.dylib:/Applications/Slicer3-3.5a/lib/vtkTe
>> em:/Applications/Slicer3-3.5a/lib/Teem-1.10.0
>>
>> Also you may have to launch X11 first before starting slicer, as it
>> sets different environment variables than "terminal".
>>
>>
>> ______________________________________________
>> DOMINIK MEIER, PH.D.
>> Assistant Professor of Radiology, Harvard Medical School
>> Center for Neurological Imaging, Brigham & Women's Hospital
>> 221 Longwood Avenue, RF396, Boston, MA 02115
>> Phone: 617 278-0800
>> Fax: 617 264-5154
>>
>>
>>
>> On Jan 18, 2010, at 7:47 PM, Dianne Patterson wrote:
>>
>>> I tarred up my old Slicer dir (version 3.2) and untarred the new
>>> Slicer (3.4.2-2010-01-06-darwin-x86.tar.gz)
>>> I'm on Mac OSX Leopard on an Intel Mac Pro.
>>>
>>> When I try to start slicer, it goes down into the bin and grabs
>>> Slicer3-real, which apparently it cannot start.
>>> If I force it to grab Slicer3 from the main Slicer directory, it will
>>> start, but this feels like a hack..
>>> I don't see any mention of the issue online, so I wanted to let you know.
>>>
>>> [seth:/usr/local 275] % Slicer3
>>> dyld: Library not loaded:
>>> /Users/hayes/Slicer-3-4/Slicer3-lib/teem-build/bin/libteem.1.dylib
>>> Referenced from: /usr/local/Slicer/bin/Slicer3-real
>>> Reason: image not found
>>> Trace/BPT trap
>>> --------
>>>
>>> Thankyou,
>>>
>>> Dianne
>>>
>>>
>>> --
>>> Dianne Patterson, Ph.D.
>>> [hidden email] <mailto:[hidden email]>
>>> University of Arizona
>>> SLHS 328
>>> 621-5105
>>> _______________________________________________
>>> slicer-users mailing list
>>> [hidden email] <mailto:[hidden email]>
>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>> To unsubscribe: send email to
>>> [hidden email]
>>> <mailto:[hidden email]> with
>>> unsubscribe as the subject
>>
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email] <mailto:[hidden email]>
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to
>> [hidden email] with unsubscribe as the
>> subject
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject