[Camino-users] datasynth ERROR on sequence parameters

[Alessandro Calamuneri]

Hi camino experts,


I need help becaues i am not able to create synthetic data using datasynth
command; so far I am basically following examples within the command
itself.


At this step I am simulating a number of voxels using a cyilinder geometry
with square packing. This is what is written in the manual of datasynth


*datasynth -schemefile tensorDirs_b=500.scheme -voxels 10000 -walkers
100000 -tmax 1000 -p 0.0 -initial uniform -snr 16.0 -G 0.022 -del 0.032
-DEL 0.04 -geometry cylinder -packing SQUARE -cylinderrad 1.9E-6
-cylindersep 4E-6 > MCdata.Bfloat*


which I suppose having something strange, because schemefile was not
written out; furthermore there is a tensorDirs_b option that I was not able
to understand, it is not on the list. What does it stand for?


However, looking at the example scanner parameters details, I have created
a scheme file with 10 b0 acquisitions and 61 diffusion weighted directions
and the same bvalue as estimated from parameters inserted.


Thus, I type


*datasynth -schemefile scheme.scheme -voxels 10000 -walkers 100000 -tmax
1000 -G 0.022 -del 0.032 -DEL 0.04 -geometry cylinder -packing SQUARE
-cylinderrad 1.9E-6 -cylindersep 4E-6 -diffusivity 2E-09 -noisetype rician
-snr 16.0 -p 0.0 -initial uniform > MCdata.Bfloat*

But I get the following error

*Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing*

*WARNING: WARNING: couldn't parse arg 10: '-G'*

*Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing*

*WARNING: WARNING: couldn't parse arg 11: '0.022'*

*Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing*

*WARNING: WARNING: couldn't parse arg 12: '-del'*

*Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing*

*WARNING: WARNING: couldn't parse arg 13: '0.032'*

*Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing*

*WARNING: WARNING: couldn't parse arg 14: '-DEL'*

*Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing*

*WARNING: WARNING: couldn't parse arg 15: '0.04'*

*Exception in thread "main" java.lang.ClassCastException:
imaging.B_VectorScheme cannot be cast to imaging.SimulableScheme*

*                at
tools.CL_Initializer.initDataSynthesizerFromSimulation(CL_Initializer.java:2031)*

*                at
tools.CL_Initializer.initDataSynthesizer(CL_Initializer.java:2121)*

*                at apps.SyntheticData.initOptions(SyntheticData.java:55)*

*                at apps.Executable.<init>(Executable.java:24)*

*                at apps.SyntheticData.<init>(SyntheticData.java:34)*

*                at apps.EntryPoint.getExecutable(EntryPoint.java:222)*

*                at apps.EntryPoint.main(EntryPoint.java:282)*


There is something wrong with the scheme, as I do not see mistyping errors.
I then discarded my scheme file and created a scheme on the fly using
options *fixedbvalue *and *fixedqmod*, hence the following


*datasynth -fixedbvalue 10 61 1.0124E+09 -voxels 10000 -walkers 100000
-tmax 1000 -G 0.022 -del 0.032 -DEL 0.04 -geometry cylinder -packing SQUARE
-cylinderrad 1.9E-6 -cylindersep 4E-6 -diffusivity 2E-09 -noisetype rician
-snr 16.0 -p 0.0 -initial uniform> MCdata.Bfloat*


*datasynth -fixedmodq 10 61 1.8578E+05 0.04 -voxels 10000 -walkers 100000
-tmax 1000 -G 0.022 -del 0.032 -DEL 0.04 -geometry cylinder -packing SQUARE
-cylinderrad 1.9E-6 -cylindersep 4E-6 -diffusivity 2E-09 -noisetype rician
-snr 16.0 -p 0.0 -initial uniform> MCdata.Bfloat*


Same error occur. What is wrong?

As far as I know, bvalue is given by the formula


b=(gamma*delta*G)^2*(DELTA-delta/3)=q^2*(DELTA-delta/3)

where gamma should be 42e6*2*pi. All units follow SI


Can you help me understanding why the command is not running? Is my formula
wrong?


Best,

Alessandro
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