3D Varian FDF file problem

[deutschmed]

Hi,

I am trying to open MRI images with the multi FDF opener plugin. I can open the files (i.e. the plugin runs) but the images are all black. This includes 2D and 3D images.

What can I do to display the images?

Thanks so much for the help!

[Daniel James White]

Hi Hannes

Begin forwarded message:

> Date:    Thu, 25 Feb 2010 11:20:47 -0800
> From:    deutschmed <[hidden email]>
> Subject: 3D Varian FDF file problem
>
> Hi,
>
> I am trying to open MRI images with the multi FDF opener plugin. I  
> can open
> the files (i.e. the plugin runs) but the images are all black. This  
> includes
> 2D and 3D images.
>
> What can I do to display the images?
>

did you try to adjust the brightness and contrast
(image - adjust - brightness contrast)
the auto button might get you close.

are all the pixels of value 0?  - look on the main tool bar window as  
you move the mouse pointer over the image


> Thanks so much for the help!
>


no probs


this plugins code might be good to include in bio-formats,,, Curtis?


Dan




Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net                BioImageXD
http://pacific.mpi-cbg.de                Fiji (is just ImageJ - batteries included)
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )

[ctrueden]

Hi Dan & Hannes,

We would be interested in adding support for FDF to Bio-Formats, as long as
we can get some sample data. Hannes, would you be able to send any our way?

Thanks,
Curtis

On Fri, Feb 26, 2010 at 3:01 AM, Dan White <[hidden email]> wrote:

> Hi Hannes
>
> Begin forwarded message:
>
>  Date:    Thu, 25 Feb 2010 11:20:47 -0800
>> From:    deutschmed <[hidden email]>
>> Subject: 3D Varian FDF file problem
>>
>>
>> Hi,
>>
>> I am trying to open MRI images with the multi FDF opener plugin. I can
>> open
>> the files (i.e. the plugin runs) but the images are all black. This
>> includes
>> 2D and 3D images.
>>
>> What can I do to display the images?
>>
>>
> did you try to adjust the brightness and contrast
> (image - adjust - brightness contrast)
> the auto button might get you close.
>
> are all the pixels of value 0?  - look on the main tool bar window as you
> move the mouse pointer over the image
>
>
>
>  Thanks so much for the help!
>>
>>
>
> no probs
>
>
> this plugins code might be good to include in bio-formats,,, Curtis?
>
>
> Dan
>
>
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Processing and Analysis
> Light Microscopy Facility
>
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> [phone] (German Mobile)
> +49  (0)351 210 2627 (Work phone at MPI-CBG)
> +49  (0)351 210 1078 (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net               BioImageXD
> http://pacific.mpi-cbg.de               Fiji (is just ImageJ - batteries
> included)
>
> http://www.chalkie.org.uk
> [hidden email]
> ( [hidden email] )
>
>
>
>
>
>
>

[deutschmed]

Hi Curtis,

thanks for our help and interest.
Absolutely. I can send you two MRI datasets acquired with a Varian scanner. The first one is a 2D data set, the second one a 3D data set.

Please send me your email address so I can email you the files.


Hannes

[nikolovi]

Hello,
I am having the same problem. When on my Mac i can view a 3d data set fine, but when i load the same fdf file on my PC (64-bit) i have black screen too. There are values between 10-30 and 10E-10 and when scaled give a nice image of noise.

The parameter from the file get loaded fine, and the fdf plugin appears to work.

Any suggestions would be helpful.
Thanks,
-Robert

[Robert Nikolov]

Hello,
I am having the same problem. When on my Mac i can view a 3d data set fine, but when i load the same fdf file on my PC (64-bit) i have black screen too. There are values between 10-30 and 10E-10 and when scaled give a nice image of noise.

The parameter from the file get loaded fine, and the fdf plugin appears to work. I suspect it has somethig to do with the 64 bit version i am running

Any suggestions would be helpful.
Thanks,
-Robert