[Camino-users] datasynth ERROR with bvector scheme

[stefania oliviero]

Thanks a lot Matt, I didn't understand this. 

From: matt.hall at ucl.ac.uk
To: stefania.oliviero at hotmail.it
CC: camino at cs.ucl.ac.uk
Subject: RE: [Camino-users] datasynth ERROR with bvector scheme
Date: Fri, 17 Oct 2014 14:15:32 +0000









Hi Stefania,
 
Because simulations calculate an explicit phase shift for each spin based on its trajectory through the substrate, they need to know more details of the pulse
 sequence than is available from the scheme you are using. You need to specify G, delta and DELTA (not just b-value and gradient direction). The BVECTOR format doesn’t have enough information (its not a “simulable scheme” and so the simulation complains.
 
Matt.
 


From: camino-users-bounces at www.nitrc.org [mailto:camino-users-bounces at www.nitrc.org]
On Behalf Of stefania oliviero

Sent: 17 October 2014 15:05

To: camino-users at www.nitrc.org

Subject: [Camino-users] datasynth ERROR with bvector scheme


 

Hi all users

I also have a problem with datasynth.

I'm using this command to generate a substrate.



datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -geometry inflammation -numcylinders ${NUMCYL} -p 0.02 -initial uniform -seed ${INT_rnd} -voxels 1 -increments 1 -separateruns -latticesize
 ${LATSIZE} -schemefile ${SCHEMEFILE} -gamma ${GAMA} ${GAMB} -diffusivity ${DIFF} -substrateinfo -drawcrosssection ${FNAMEINFO}.gray > ${OUTPUTDIR}/${FNAME} 2> ${FNAMEINFO}.txt




When I use a scheme file with a stejskaltanner format It works.

If I try to use a scheme file with a bvector format It doesn't work and the follow error appears:



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)



The scheme file in bvector format is that downloaded from the tutorial DTI 4Ddwi_bvector.scheme:
#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
 What is the problem? Where am I doing wrong?

Thanks for interest.



Best regards

Stefania Oliviero

 		 	   		  
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