[Camino-users] linrecon - qball

[Daniel Alexander]

Check the sizes of your files, because one of them is not what linrecon expects; most likely the data file, as the errors suggests it wants 257 values per voxel.  In particular, qball.Bfloat should have size <in-plane resolution>x<num slices>x257x4 bytes.

Otherwise it may be a problem with the mask, which needs to match the size of the data volume.  Try removing the -header argument and/or the -bgmask and see if that helps.  That will at least pinpoint the problem.

Danny


On 23 Apr 2012, at 13:24, Curci Marina Carmela wrote:

> Hello to everyone!!
> Today I have a problem with qball ODF reconstruction.
> My qball dataset has 257 volumes and in the schemefile I have also 257 directions.
> I copy here the lines appeared in my terminal:
> 
> 
> marina at marina-desktop:~/Desktop/camino/QBALL_RAWDATA$ linrecon qball.Bfloat SIEMENS256.scheme matrixrecon.Bdouble -bgmask /home/marina/Desktop/fsmask_1mm_resamp2x2x2.nii.gz -header QBALL.nii.gz > ODF.Bdouble
> 
> 
> Apr 23, 2012 2:20:23 PM misc.LoggedException logException
> SEVERE: Exception in thread "main" class data.DataSourceException: End of file reached without completing voxel.
> 	at data.VoxelOrderDataSource.readNextVoxel(VoxelOrderDataSource.java:279)
> 	at data.VoxelOrderDataSource.nextVoxel(VoxelOrderDataSource.java:189)
> 	at inverters.LinearInversion.<init>(LinearInversion.java:70)
> 	at apps.LinearRecon.initVariables(LinearRecon.java:39)
> 	at apps.Executable.<init>(Executable.java:28)
> 	at apps.ModelFit.<init>(ModelFit.java:49)
> 	at apps.LinearRecon.<init>(LinearRecon.java:30)
> 	at apps.EntryPoint.getExecutable(EntryPoint.java:124)
> 	at apps.EntryPoint.main(EntryPoint.java:273)
> 
> Could not read the matrix.  Expecting 257 elements per row.
> Exception in thread "main" java.lang.RuntimeException: data.DataSourceException: End of file reached without completing voxel.
> 	at inverters.LinearInversion.<init>(LinearInversion.java:75)
> 	at apps.LinearRecon.initVariables(LinearRecon.java:39)
> 	at apps.Executable.<init>(Executable.java:28)
> 	at apps.ModelFit.<init>(ModelFit.java:49)
> 	at apps.LinearRecon.<init>(LinearRecon.java:30)
> 	at apps.EntryPoint.getExecutable(EntryPoint.java:124)
> 	at apps.EntryPoint.main(EntryPoint.java:273)
> Caused by: data.DataSourceException: End of file reached without completing voxel.
> 	at data.VoxelOrderDataSource.readNextVoxel(VoxelOrderDataSource.java:279)
> 	at data.VoxelOrderDataSource.nextVoxel(VoxelOrderDataSource.java:189)
> 	at inverters.LinearInversion.<init>(LinearInversion.java:70)
> 	... 6 more
> 
> Could you help me please?
> Thank you,
> Marina
> 
> 
> 
> 
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