[Camino-users] Camino r1010 dtlutgen troubleshooting

[Irvin Teh]

Dear Phil,

Thanks a lot. I've reverted to 1.6 and it works fine.

What I missed out before was doing a make clean.

Cheers,

Irvin

________________________________________
From: Philip A Cook [cookpa at mail.med.upenn.edu]
Sent: Tuesday, September 06, 2011 10:29 PM
To: Irvin Teh
Cc: camino-users at www.nitrc.org
Subject: Re: [Camino-users] Camino r1010 dtlutgen troubleshooting

I can reproduce this error using JDK 1.7 on Linux, but it works fine for me using JDK 1.6 on both Linux and Mac.

Maybe your system was still using 1.7 instead of 1.6? To use 1.6, you would need to prepend it to the PATH so that "java -version" runs 1.6. Then you would have to do

cd camino
make clean; make

It seems that Java 7 has dropped the usual Java policy of strict backwards compatibility. We usually keep current with the latest Java so we will be working on supporting Java 7, in the interim I would advise everyone to use 1.6.

Thanks,


Phil

On Sep 5, 2011, at 11:08 PM, Irvin Teh wrote:

> Dear Phil,
>
> Thanks for the reply. Yes downloaded the JDK1.7.0 RPM from the Oracle website. Also tried the self JDK1.6.0_27 self extracting binary.
>
>> [irvin at host brain]$ java -version
>> java version "1.7.0"
>> Java(TM) SE Runtime Environment (build 1.7.0-b147)
>> Java HotSpot(TM) 64-Bit Server VM (build 21.0-b17, mixed mode)
>
> Any help would be much appreciated.
>
> Irvin
>
> ________________________________________
> From: Philip A Cook [cookpa at mail.med.upenn.edu]
> Sent: Friday, September 02, 2011 2:46 AM
> To: Irvin Teh
> Cc: camino-users at www.nitrc.org
> Subject: Re: [Camino-users] Camino r1010 dtlutgen troubleshooting
>
> Hi Irvin,
>
> Are you using Sun Java? Can you please check with
>
> java -version?
>
> Thanks,
>
>
> Phil
>
> On Sep 1, 2011, at 6:40 AM, Irvin Teh wrote:
>
>> Hi all,
>>
>> Was wondering if anyone can help on an issue I've been facing while trying to migrate using camino from a Windows XP-Cygwin-camino_v2_880 setup I've been using previously, to a Red Hat Linux x86_64-camino_r1010 setup. Calculating the diffusion tensor and q-ball work fine, but I've been getting errors (See below) when trying to run dtlutgen. I've tried swapping between java versions jdk1.7.0 and jdk1.6.0_27, with no luck.
>>
>> Would be very grateful if someone might know a fix for this, thanks!
>>
>> Irvin
>> Singapore
>>
>>
>> [irvin at host brain]$ dtlutgen -schemefile dvec.scheme -snr 16.0 -inversion 1 > picoTable.dat
>> Exception in thread "main" java.lang.NullPointerException
>>       at numerics.MTRandom.next(MTRandom.java:342)
>>       at java.util.Random.nextDouble(Random.java:438)
>>       at tractography.DT_LookupTableGenerator.initializeEigenvectors(DT_LookupTableGenerator.java:390)
>>       at tractography.DT_LookupTableGenerator.<init>(DT_LookupTableGenerator.java:77)
>>       at tractography.OneTensorLUTGenerator.<init>(OneTensorLUTGenerator.java:32)
>>       at apps.GenerateDTLUT.execute(GenerateDTLUT.java:270)
>>       at apps.EntryPoint.main(EntryPoint.java:266)
>>
>> [irvin at host brain]$ java -version
>> java version "1.7.0"
>> Java(TM) SE Runtime Environment (build 1.7.0-b147)
>> Java HotSpot(TM) 64-Bit Server VM (build 21.0-b17, mixed mode)
>>
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>