[ome-users] MINC (.mnc) MRI image files: error message when importing

[Melissa Linkert]

Hi,

> I was trying to use the Bio-Formats MINC (.mnc) file import via the ImageJ (Fiji) plugin to read the sample files at:
> https://bigbrain.loris.ca/
> 
> Every single MINC file I tested failed, and gave a similar error as noted below.
> 
> Note that the NIfTI (.nii) versions of the same datasets worked perfectly fine (after manually extracting from the .gz file).
> 
> You should be able to sign up for access to the above website, and get plenty of test images and metadata.
> 
> Tested:
> LOCI Plugins for ImageJ, revision 34f3393, built 7 May 2013 Release: 4.4.9-DEV
> as well as:
> (trunk) LOCI Plugins for ImageJ, revision 34aa07c, built 9 July 2013 Release: 4.5-DEV
> 

Thank you for reporting this problem.  I have been able to access files
from the BigBrain website, and can confirm the problem.

I have opened this ticket on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/11257

If you would like to receive an automated email each time the ticket is
updated, please let me know and I will CC you.

Regards,
-Melissa

On Tue, Jul 09, 2013 at 02:04:50PM -0700, K F wrote:
> I was trying to use the Bio-Formats MINC (.mnc) file import via the ImageJ (Fiji) plugin to read the sample files at:
> https://bigbrain.loris.ca/
> 
> Every single MINC file I tested failed, and gave a similar error as noted below.
> 
> Note that the NIfTI (.nii) versions of the same datasets worked perfectly fine (after manually extracting from the .gz file).
> 
> You should be able to sign up for access to the above website, and get plenty of test images and metadata.
> 
> Tested:
> LOCI Plugins for ImageJ, revision 34f3393, built 7 May 2013 Release: 4.4.9-DEV
> as well as:
> (trunk) LOCI Plugins for ImageJ, revision 34aa07c, built 9 July 2013 Release: 4.5-DEV
> 
> 
> Both versions gave almost identical error result.  The following is pasted from the 4.5 revision 34aa07c trunk build:
> 
> (Fiji Is Just) ImageJ 1.47v; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 38MB of 2989MB (1%)
>  
> java.lang.reflect.InvocationTargetException
>     at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
>     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>     at java.lang.reflect.Method.invoke(Method.java:597)
>     at ij.Command.runPlugIn(Command.java:148)
>     at ij.Command.runCommand(Command.java:97)
>     at ij.Executer.run(Executer.java:64)
>     at java.lang.Thread.run(Thread.java:662)
> Caused by: java.lang.NullPointerException
>     at loci.formats.services.NetCDFServiceImpl.getArray(NetCDFServiceImpl.java:174)
>     at loci.formats.services.NetCDFServiceImpl.getVariableValue(NetCDFServiceImpl.java:156)
>     at loci.formats.in.MINCReader.initFile(MINCReader.java:161)
>     at loci.formats.FormatReader.setId(FormatReader.java:1183)
>     at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
>     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
>     at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>     at loci.plugins.in.Importer.run(Importer.java:79)
>     at loci.plugins.LociImporter.run(LociImporter.java:81)
>     at ij.IJ.runUserPlugIn(IJ.java:195)
>     at ij.IJ.runPlugIn(IJ.java:160)
>     ... 7 more

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