[Camino-users] Problem in getting a correct FA map

[apisheh]

Dear All,

I am having a problem in getting a correct FA map. Here is the summary of what I have done to find this map.
 
1. Converting the data to NifTI:
      dcm2nii dcm_file

2. Making Scheme File
      pointset2scheme -bvalue bvalue_file < grad_dirs_file > dwi_bvector_scheme_file

3. Convert the DWI data
      image2voxel -4dimage raw_dwi_nii_file -outputfile dwi_Bfloat_file

4. Fit the diffusion tensor
      dtfit dwi_Bfloat_file dwi_bvector_scheme_file -outputfile dt_Bdouble_file

5. Compute Fractional Anisotropy & Mean Diffusivity Maps
      for PROG in fa md; do
         cat dt_Bdouble_file | ${PROG} | voxel2image -outputroot ${PROG} -header raw_dwi_nii_file
      done

6. Compute the Eigen System
      cat dt_Bdouble_file | dteig > dt_eig_Bdouble_file

7. Checking the orientation
      pdview -inputfile dt_eig_Bdouble_file -scalarfile fa_nii_file


Also, I have checked any potential problem with dwi volume data using ITK-SNAP and the data seems to be fine. Could someone kindly help me how I can determine any potential problem in the scheme file, which I have brought in below? Thank you in advance for your time and consideration of my problem.

#B-vector scheme. Contains gradient directions and b-values
#g_xg_yg_zb
VERSION: BVECTOR
   0.000000  -0.896569  -0.442905   1.000E03
   0.128542  -0.984420   0.119973   1.000E03
   0.800509  -0.596441  -0.058681   1.000E03
  -0.881053  -0.425170  -0.207307   1.000E03
  -0.474272   0.543437   0.692635   1.000E03
   0.391668   0.638172  -0.662822   1.000E03
  -0.524076   0.231131   0.819709   1.000E03
  -0.463732   0.563601  -0.683598   1.000E03
  -0.855062   0.117571  -0.505021   1.000E03
  -0.866833  -0.365917  -0.338681   1.000E03
  -0.938289   0.116876   0.325506   1.000E03
   0.000000   0.000000   1.000000   1.000E03
   0.668797  -0.345354  -0.658363   1.000E03
  -0.220695   0.283350   0.933277   1.000E03
   0.118224  -0.687707  -0.716297   1.000E03
  -0.623284  -0.444008   0.643719   1.000E03
  -0.010828  -0.989984   0.140763   1.000E03
  -0.222798  -0.788292   0.573547   1.000E03
   0.834059   0.268739  -0.481793   1.000E03
   0.512966  -0.250867  -0.820933   1.000E03
  -0.310584  -0.512977   0.800245   1.000E03
   0.874804   0.373180  -0.308958   1.000E03
   0.000000   0.000000   0.000000   0.000E00
   0.689039  -0.194531   0.698129   1.000E03
   0.442299   0.896697  -0.017477   1.000E03
   0.749844   0.210447  -0.627253   1.000E03
  -0.624818   0.757523   0.189104   1.000E03
  -0.767869   0.272113  -0.579941   1.000E03
  -0.810237  -0.401922  -0.426585   1.000E03
   0.507114  -0.804687   0.308732   1.000E03
   0.589042  -0.734014   0.338013   1.000E03
  -0.556982   0.727640  -0.400389   1.000E03
   0.065044  -0.717700   0.693308   1.000E03
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