[Camino-users] Error converting large DWI file

[Elizabeth Zakszewski]

I double-checked that I was using an updated version (r-1205), and tried
running it again with image2voxel (which I realized is actually the correct
command for what I want to do), but got the same error.


On Mon, May 13, 2013 at 1:33 PM, Philip A Cook <cookpa at mail.med.upenn.edu>wrote:

> Hi,
>
> The line numbers in the exception aren't lining up for me so I suspect you
> have an older version of the code. Updating might help. There might be some
> counter in the NIfTI class that is overflowing. I've redone a bunch of that
> code in the current version, so maybe it will work now. If that's not an
> option I can check out the version you have, if you can tell me the
> revision number.
>
>
> On May 13, 2013, at 2:16 PM, Elizabeth Zakszewski wrote:
>
> > Hello,
> >
> > I have a DWI .nii file that is 3.4G.  I had to increase the Java heap
> size in niftidt2camino to 50G in order to get it to run (our server should
> be able to handle 96G). But the conversion still terminates with the
> following error:
> >
> > NIFTI to CAMINO, this wil convert the data from scanner order to voxel
> order
> > May 13, 2013 1:06:38 PM misc.LoggedException logException
> > SEVERE: Exception in thread "main" class misc.LoggedException:
> java.io.IOException: Negative seek offset
> >         at
> imaging.Nifti1Dataset.getImageDataSource(Nifti1Dataset.java:2608)
> >         at apps.DT_ToCamino.main(DT_ToCamino.java:82)
> >
> > Exception in thread "main" misc.LoggedException: java.io.IOException:
> Negative seek offset
> >         at
> imaging.Nifti1Dataset.getImageDataSource(Nifti1Dataset.java:2608)
> >         at apps.DT_ToCamino.main(DT_ToCamino.java:82)
> > Caused by: java.io.IOException: Negative seek offset
> >         at java.io.RandomAccessFile.seek(Native Method)
> >         at imaging.Nifti1Dataset.readVolBlob(Nifti1Dataset.java:2177)
> >         at imaging.Nifti1Dataset.readDoubleVol(Nifti1Dataset.java:1912)
> >         at
> imaging.Nifti1Dataset.getImageDataSource(Nifti1Dataset.java:2591)
> >         ... 1 more
> >
> >
> > We have never seen a Negative seek offset error before and aren't sure
> how to troubleshoot. Is there a way to correct this, or a better way to
> convert a large file?
> >
> > Thanks,
> > Liz
> > _______________________________________________
> > Camino-users mailing list
> > Camino-users at www.nitrc.org
> > http://www.nitrc.org/mailman/listinfo/camino-users
>
>
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