[Camino-users] datasynth ERROR on sequence parameters

[Alessandro Calamuneri]

Hi David,
it worked out now. Thanks a lot!

Alessandro

2014-10-16 13:45 GMT+02:00 Slater David <David.Slater at chuv.ch>:

>  Hi Alessandro,
>
>
>
> I think your problem is coming from the scheme file you are using. Try
> creating a Stejskal-Tanner scheme as described here:
> http://cmic.cs.ucl.ac.uk/camino//index.php?n=Docs.SchemeFiles
> <http://cmic.cs.ucl.ac.uk/camino/index.php?n=Docs.SchemeFiles>. It should
> take the following form:
>
>
>
> VERSION: STEJSKALTANNER
>
> x_1 y_1 z_1 |G_1| DELTA_1 delta_1 TE_1
>
> x_2 y_2 z_2 |G_2| DELTA_2 delta_2 TE_2
>
> :
>
> :
>
> x_N y_N z_N |G_N| DELTA_N delta_N TE_N
>
>
>
> Save it as something like *‘myscheme.scheme’*. This type of scheme file
> contains the gradient pulse information so you can remove these options
> from the *datasynth* command. Thus the following command will output
> synthetic data in .txt format:
>
>
>
> datasynth -schemefile myscheme.scheme -voxels 10000 -walkers 100000 -tmax
> 1000 -geometry cylinder -packing SQUARE -cylinderrad 1.9E-6 -cylindersep
> 4E-6 -diffusivity 2E-09 -noisetype rician -snr 16.0 -p 0.0 -initial
> uniform  | float2txt > SIMdata.txt
>
>
>
> Note that I have removed the *–G*, *–del* and *–DEL* options which were
> causing you errors and used the *float2txt* command to get the output in
> .txt format.
>
>
>
> Try this with a corrected scheme file and you should get your synthetic
> voxel data.
>
>
>
> Best,
>
> David
>
>
>
>
>
> *De :* camino-users-bounces at www.nitrc.org [mailto:
> camino-users-bounces at www.nitrc.org] *De la part de* Alessandro Calamuneri
> *Envoyé :* 16 October 2014 12:21
> *À :* camino-users at www.nitrc.org
> *Objet :* [Camino-users] datasynth ERROR on sequence parameters
>
>
>
> 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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