Question

[Scott Wilson-10]

What operating system (the more details the better) makes this program run and function the best?  Price isn't much of an issue (under $15,000) and the measurements that we will be doing are of intervertebral disc spaces in rabbits acquired via X-ray and then scanned into image file.  While this is the primary application we would like to use it for various other applications (including µCT, staining, etc.).

 

Thanks,

 

Scott T. Wilson, B.S., LAT

Associate Study Director

MPI Research

54943 N. Main St.

Mattawan, MI 49071

phone:  [phone] ex. 1610

fax:  [phone]

email:  [hidden email]

 


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[Albert Cardona]

Scott Wilson wrote:
> What operating system (the more details the better) makes this program run and function the best?  Price isn't much of an issue (under $15,000) and the measurements that we will be doing are of intervertebral disc spaces in rabbits acquired via X-ray and then scanned into image file.  While this is the primary application we would like to use it for various other applications (including µCT, staining, etc.).
>  


In my experience:

- MacOSX is best if you are NOT planning to push the limits of the
machine. OS integration for dialogs and widgets is just perfect. For
high memory loads, MacOSX  pages a lot (uses virtual memory a lot, which
slows down everything). Memory allocatin with Xmx should NEVER go beyond
66% of actual RAM in the machine, or it will start paging immediately.
Also, MacOSX has only a beta for java 1.6.0 and only 1.5.0 for Leopard.

- Windows is ok as well for 32-bit, which limits you to 1700 Mb of RAM.
The 64-bit java versions for windows have plenty of memory corruption
problems. Macros unexpectedly fail after several runs, separate
instances of ImageJ mix up dialogs one from the other, and the like.
Needs to be restarted often, and nearly always with a "Terminate" from
the Task Manager.

- Linux with 64-bit java is best if you need to get the most of your
hardware. Best memory usage by far, lets you use 99% of the available
RAM without paging. But it comes at the price of poor integration with
the OS: I/O dialogs are loathsome (but at least you can use drag and
drop from nautilus and konqueror), and the look and feel doesn't match.


For my purposes of massive image registration and 3D modeling Linux
64-bit is just right. You'll have to
 decide what set of features best suit your needs.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Jonathan Hilmer]

A topic that seems to appear regularly on this list is a general
problem with having enough memory or dealing with large image sets.
Considering your price range, I would look at using a product like the
HyperDrive that adapts desktop memory to be used as though it were a
hard disk: paging then becomes a non-issue.

http://www.hyperdrive4.com/
http://www.tomshardware.com/2007/11/07/hyperdrive_4_redefines_solid_state_storage/index.html



Jonathan


On Dec 3, 2007 8:45 AM, Scott Wilson <[hidden email]> wrote:

> What operating system (the more details the better) makes this program run and function the best?  Price isn't much of an issue (under $15,000) and the measurements that we will be doing are of intervertebral disc spaces in rabbits acquired via X-ray and then scanned into image file.  While this is the primary application we would like to use it for various other applications (including µCT, staining, etc.).
>
>
>
> Thanks,
>
>
>
> Scott T. Wilson, B.S., LAT
>
> Associate Study Director
>
> MPI Research
>
> 54943 N. Main St.
>
> Mattawan, MI 49071
>
> phone:  [phone] ex. 1610
>
> fax:  [phone]
>
> email:  [hidden email]

[Adam Hacking]

Scott,

We do a lot of uCT analysis and ImageJ work and put our own system together.

It cost around 1500 is and very adequate.

We use Skyscan software and there stuff is optimized for Intel processors. This software has a nice batch manager so you can set ity up to run overnight and process a bunch of samples. Anyhow for the uCT we use 64 bit windows XP, 4GB RAM, intel duo processor, fast memory and fast harddrives.

If you want to spend more money you can set up a Linux cluster and get a license for the software, but unless you are doing a large volume  of work I don't think its worth it. One other solution is to use a box for reconstruction and a boc for analysis.

We perform basic bone image analysis with ImageJ and this setup is fine.

Adam


Scott Wilson <[hidden email]> wrote: What operating system (the more details the better) makes this program run and function the best?  Price isn't much of an issue (under $15,000) and the measurements that we will be doing are of intervertebral disc spaces in rabbits acquired via X-ray and then scanned into image file.  While this is the primary application we would like to use it for various other applications (including µCT, staining, etc.).

 

Thanks,

 

Scott T. Wilson, B.S., LAT

Associate Study Director

MPI Research

54943 N. Main St.

Mattawan, MI 49071

phone:  [phone] ex. 1610

fax:  [phone]

email:  [hidden email]

 


This communication, including attachments, is for the exclusive use of addressee and
may contain proprietary, confidential and/or privileged information. If you are not
the intended recipient, any use, copying, disclosure, dissemination or distribution
is strictly prohibited. If you are not the intended recipient, please notify the sender
immediately by return e-mail, delete this communication and destroy all copies.




________________________________________________________________         Dr. S Adam Hacking, Post Doctoral Fellow
JTN Wong Laboratories for Mineralized Tissue Research,
Center for Bone and Periodontal Research,
McGill University     740 Dr. Penfield Ave. Rm. 2300A
Montreal, QC, Canada H3A 1A4
Ph.:  514-398-5112
Fax: [phone]

[Aryeh Weiss]

Albert Cardona wrote:

>
> - Windows is ok as well for 32-bit, which limits you to 1700 Mb of RAM.

Please note that with the JRockit JVM it is possible to use more memory. I use
2.3GB and have tried it successfully close to the 3GB that my machine has.

See http://dev2dev.bea.com/blog/hstahl/archive/2005/12/how_to_get_almo.html
to see how to do it and point ImageJ to the JRockit JVM.

You also have to move the tools.jar file to a suitable Java extension folder.

So far I have not experienced any strangness with it.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]