[Camino-users] Information

Tue May 9 09:25:37 PDT 2017

This error either means the scheme file is bad, or (less commonly) the data is bad. If the scheme file contains N measurements, the data file has to contain exactly X * Y * Z * N values, for an image of dimensions X Y Z. If this isn't the case, you get this error.

In your case, the scheme file looks wrong. It not only has missing values, but the gradients are different. When I run the DTI tutorial code

  pointset2scheme -inputfile grad_dirs.txt -bvalue 1E9 -outputfile 4Ddwi_b1000_bvector.scheme

I get the expected result

#B-vector scheme. Contains gradient directions and b-values
#g_x	g_y	g_z	b
VERSION: BVECTOR
   0.000000   0.000000   0.000000   0.000E00
   0.557286   0.673159  -0.486096   1.000E09
   0.411008  -0.525405  -0.744998   1.000E09
  -0.576000   0.585141  -0.570819   1.000E09
  -0.058952  -0.998228   0.008080   1.000E09
   0.671827  -0.643902  -0.366113   1.000E09
  -0.147877   0.617325  -0.772685   1.000E09
  -0.527370   0.221392  -0.820285   1.000E09
   0.091543  -0.251136  -0.963613   1.000E09
  -0.850415  -0.498192   0.169112   1.000E09
  -0.764016  -0.584574  -0.273045   1.000E09
   0.000000   0.000000   0.000000   0.000E00
   0.300301   0.470652  -0.829642   1.000E09
  -0.527168  -0.551126  -0.646804   1.000E09
   0.723852   0.265109  -0.636989   1.000E09
  -0.878656   0.262998  -0.398492   1.000E09
  -0.286924   0.886166  -0.363848   1.000E09
   0.938309  -0.334647  -0.087105   1.000E09
  -0.397842   0.913244   0.087796   1.000E09
  -0.085190  -0.635081  -0.767733   1.000E09
   0.307272   0.873671   0.377204   1.000E09
   0.448367   0.003264  -0.893843   1.000E09
   0.000000   0.000000   0.000000   0.000E00
   0.955559   0.060361  -0.288553   1.000E09
  -0.157881  -0.866147   0.474197   1.000E09
   0.178264  -0.864319  -0.470292   1.000E09
  -0.510729  -0.858184   0.051732   1.000E09
   0.726454  -0.673055   0.138787   1.000E09
  -0.059404   0.198388  -0.978322   1.000E09
  -0.368122  -0.199753  -0.908067   1.000E09
  -0.777683  -0.149878  -0.610528   1.000E09
   0.762668  -0.240762  -0.600309   1.000E09
   0.973096   0.146769   0.177601   1.000E09

> On May 9, 2017, at 6:24 AM, Stefano Sirgiovanni <stefano.sirgiovanni84 at gmail.com> wrote:
> 
> Hi,
> 
> Thank you for your answers, I'll try to see e do what you said me.
> 
> I don't know exactly what I've done but it doesn't present that problem again, but now another error appear when I use the command line:
> 
> dtfit dwi.Bfloat 4Ddwi_b1000_bvector.scheme -bgmask brain_mask.nii.gz -outputfile dt.Bdouble
> 
> the error is:
> 
> Exception in thread "main" misc.LoggedException: The data file does not contain a whole number of voxels. 
> Check the scheme file. Got Exception data.DataSourceException: End of file reached without completing voxel.
>         at apps.ModelFit.execute(
> ModelFit.java:157)
>         at apps.EntryPoint.main(
> EntryPoint.java:284)
> 
> 
> I attach to the mail the scheme file.
> 
> Thanks again for all
> 
> Stefano Sirgiovanni
> 
> 2017-05-08 19:50 GMT+02:00 Philip A Cook <cookpa at mail.med.upenn.edu>:
> Hi,
> 
> The three numbers are the orientation of the principal direction (eigenvector with largest eigenvalue), in voxel coordinates. The number in parantheses is the value of the underlying scalar background, which by default is FA. If you'd like it to be a particular eigenvalue, you can use "-scalarfile" to use that image in place of FA.
> 
> Your error message suggests a problem with your scheme file. Since this is the example scheme file, I suspect some kind of platform dependent parsing problem. Just to be sure, can you send me your scheme file? Also, what OS you are running on, and if you have the system configured for a language other than English. These things can affect how Java processes text.
> 
> Thanks
> 
> 
> 
> > On May 7, 2017, at 8:51 AM, Stefano Sirgiovanni <stefano.sirgiovanni84 at gmail.com> wrote:
> >
> > Hi All,
> >
> >
> >
> > I'm starting to use the software Camino using Windows.
> >
> >
> >
> > I would like to ask for two information.
> >
> >
> >
> > The first information is this: when I use the pdview during the tutorial and observe the various vectors, if I place it on a voxel I get the coordinates of my position and under 4 numbers, one of this placed in the round parentheses. Are the 3 numbers  before the round parentheses the eigenvalues and the value in round parentheses the FA or MD?
> >
> >
> >
> > The second question.
> >
> >
> >
> > I tried to use the procedure used in the trial on a subject but when I came to the command:
> >
> >
> >
> > dtfit dwi.Bfloat 4Ddwi_b1000_bvector.scheme -bgmask brain_mask.nii.gz -outputfile dt.Bdouble
> >
> >
> >
> > I get this error
> >
> >
> >
> > Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
> >
> >         at java.util.Vector.elementAt(Unknown Source)
> >
> >         at imaging.DW_Scheme.readScheme(DW_Scheme.java:530)
> >
> >         at tools.CL_Initializer.initImagingScheme(CL_Initializer.java:1588)
> >
> >         at apps.ModelFit.initOptions(ModelFit.java:61)
> >
> >         at apps.Executable.<init>(Executable.java:24)
> >
> >         at apps.ModelFit.<init>(ModelFit.java:50)
> >
> >         at apps.EntryPoint.getExecutable(EntryPoint.java:142)
> >
> >         at apps.EntryPoint.main(EntryPoint.java:282)
> >
> >
> >
> >
> >
> > and it doesn’t generate dt.Bdouble file and so I can’t create the FA or MD file.
> >
> >
> >
> >
> >
> > What could it be?
> >
> >
> >
> > Thanks a lot
> >
> >
> >
> > Cheers
> >
> >
> >
> > --
> > Stefano Sirgiovanni
> > _______________________________________________
> > Camino-users mailing list
> > Camino-users at www.nitrc.org
> > http://www.nitrc.org/mailman/listinfo/camino-users
> 
> 
> 
> 
> -- 
> Stefano Sirgiovanni
> <4Ddwi_b1000_bvector.scheme>