<html><body><div style="color:#000; background-color:#fff; font-family:Courier New, courier, monaco, monospace, sans-serif;font-size:12pt"><div class="" style="">Dear All,</div><div class="" style=""><br class="" style=""></div><div class="" style="">I am having a problem in getting a correct FA map. Here is the summary of what I have done to find this map.</div><div class="" style=""> </div><div class="" style="">1. Converting the data to NifTI:</div><div class="" style=""> dcm2nii dcm_file</div><div class="" style=""><br class="" style=""></div><div class="" style="">2. Making Scheme File</div><div class="" style=""> pointset2scheme -bvalue bvalue_file < grad_dirs_file > dwi_bvector_scheme_file</div><div class="" style=""><br class="" style=""></div><div class="" style="">3. Convert the DWI data</div><div class="" style=""> image2voxel -4dimage raw_dwi_nii_file -outputfile
dwi_Bfloat_file</div><div class="" style=""><br class="" style=""></div><div class="" style="">4. Fit the diffusion tensor</div><div class="" style=""> dtfit dwi_Bfloat_file dwi_bvector_scheme_file -outputfile dt_Bdouble_file</div><div class="" style=""><br class="" style=""></div><div class="" style="">5. Compute Fractional Anisotropy & Mean Diffusivity Maps</div><div class="" style=""> for PROG in fa md; do</div><div class="" style=""> cat dt_Bdouble_file | ${PROG} | voxel2image -outputroot ${PROG} -header raw_dwi_nii_file</div><div class="" style=""> done</div><div class="" style=""><br class="" style=""></div><div class="" style="">6. Compute the Eigen System</div><div class="" style=""> cat dt_Bdouble_file | dteig > dt_eig_Bdouble_file</div><div class="" style=""><br class="" style=""></div><div class="" style="">7. Checking the
orientation</div><div class="" style=""> pdview -inputfile dt_eig_Bdouble_file -scalarfile fa_nii_file</div><div class="" style=""><br class="" style=""></div><div class="" style=""><br class="" style=""></div><div class="" style="">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.</div><div class="" style=""><br class="" style=""></div><div class="" style="">#B-vector scheme. Contains gradient directions and b-values</div><div class="" style="">#g_x<span class="" style="white-space:pre"> </span>g_y<span class="" style="white-space:pre"> </span>g_z<span class="" style="white-space:pre"> </span>b</div><div class="" style="">VERSION: BVECTOR</div><div class="" style=""> 0.000000
-0.896569 -0.442905 1.000E03</div><div class="" style=""> 0.128542 -0.984420 0.119973 1.000E03</div><div class="" style=""> 0.800509 -0.596441 -0.058681 1.000E03</div><div class="" style=""> -0.881053 -0.425170 -0.207307 1.000E03</div><div class="" style=""> -0.474272 0.543437 0.692635 1.000E03</div><div class="" style=""> 0.391668 0.638172 -0.662822 1.000E03</div><div class="" style=""> -0.524076 0.231131 0.819709 1.000E03</div><div class="" style=""> -0.463732 0.563601 -0.683598 1.000E03</div><div class="" style=""> -0.855062 0.117571 -0.505021 1.000E03</div><div class="" style=""> -0.866833 -0.365917 -0.338681 1.000E03</div><div class="" style=""> -0.938289 0.116876
0.325506 1.000E03</div><div class="" style=""> 0.000000 0.000000 1.000000 1.000E03</div><div class="" style=""> 0.668797 -0.345354 -0.658363 1.000E03</div><div class="" style=""> -0.220695 0.283350 0.933277 1.000E03</div><div class="" style=""> 0.118224 -0.687707 -0.716297 1.000E03</div><div class="" style=""> -0.623284 -0.444008 0.643719 1.000E03</div><div class="" style=""> -0.010828 -0.989984 0.140763 1.000E03</div><div class="" style=""> -0.222798 -0.788292 0.573547 1.000E03</div><div class="" style=""> 0.834059 0.268739 -0.481793 1.000E03</div><div class="" style=""> 0.512966 -0.250867 -0.820933 1.000E03</div><div class="" style=""> -0.310584 -0.512977 0.800245
1.000E03</div><div class="" style=""> 0.874804 0.373180 -0.308958 1.000E03</div><div class="" style=""> 0.000000 0.000000 0.000000 0.000E00</div><div class="" style=""> 0.689039 -0.194531 0.698129 1.000E03</div><div class="" style=""> 0.442299 0.896697 -0.017477 1.000E03</div><div class="" style=""> 0.749844 0.210447 -0.627253 1.000E03</div><div class="" style=""> -0.624818 0.757523 0.189104 1.000E03</div><div class="" style=""> -0.767869 0.272113 -0.579941 1.000E03</div><div class="" style=""> -0.810237 -0.401922 -0.426585 1.000E03</div><div class="" style=""> 0.507114 -0.804687 0.308732 1.000E03</div><div class="" style=""> 0.589042 -0.734014 0.338013
1.000E03</div><div class="" style=""> -0.556982 0.727640 -0.400389 1.000E03</div><div class="" style=""> 0.065044 -0.717700 0.693308 1.000E03</div></div></body></html>