*** empty log message ***

probtrackOptions.cc

@@ -175,7 +175,7 @@ probtrackOptions* probtrackOptions::gopt = NULL;
   
   void probtrackOptions::modehelp()
   {
-    cout<<"tracking mode -  Options are:\n\n simple (default)\n    Input is text file defining start point.\n    Output is dti space volume with connectivity values at each voxel.\n   Note-everything in simple mode is in\n    diffusion space.\n\n seeds_to_targets\n    Inputs are a volume with ones at all seed points\n    (requires a matrix taking it to DTI space (--xfm))\n    and a text file with the name of a single target mask\n    on each new line (--targetmasks).\n    Output is a single volume for each target mask where the value of each\n    volume within the seed mask corresponds to the number of particles \n    seeded from this voxel reaching this target mask.\n\n seedmask\n    Input is a volume with ones at all seed points\n    (requires a matrix taking it to DTI space (--xfm))\n    Output is seed space volume with connectivity values at each voxel\n    summed from every seed.\n\n twomasks_symm\n    Input is a binary volume for first mask (-x)\n    also requires a binary volume for second mask (--mask2)\n    (requires a matrix taking both seeds to DTI space (--xfm))\n    Output is the sum of all paths the from first mask which pass\n    through the second and vice-versa  i.e. only paths\n    which pass through both masks are retained.\n\n waypoints\n    Input is a binary volume for seed mask (-x)\n    also requires a binary waypoint mask or ascii list\n    of waypoint masks (--mask2)\n    (requires a matrix taking both seeds to DTI space (--xfm))\n    Output is a volume containing all the paths from the\n    seedmask which pass through ALL of the waypoint masks.\n"<<endl;
+    cout<<"tracking mode -  Options are:\n\n simple (default)\n    Input is text file defining start point.\n    Output is dti space volume with connectivity values at each voxel.\n   If your seed voxel is not in diffusion space\n    you need to specify a volume in yuour input\n    space (--seedref)\n   and a matrix taking this space to diffusion space(--xfm).\n\n seeds_to_targets\n    Inputs are a volume with ones at all seed points\n    (requires a matrix taking it to DTI space (--xfm))\n    and a text file with the name of a single target mask\n    on each new line (--targetmasks).\n    Output is a single volume for each target mask where the value of each\n    volume within the seed mask corresponds to the number of particles \n    seeded from this voxel reaching this target mask.\n\n seedmask\n    Input is a volume with ones at all seed points\n    (requires a matrix taking it to DTI space (--xfm))\n    Output is seed space volume with connectivity values at each voxel\n    summed from every seed.\n\n twomasks_symm\n    Input is a binary volume for first mask (-x)\n    also requires a binary volume for second mask (--mask2)\n    (requires a matrix taking both seeds to DTI space (--xfm))\n    Output is the sum of all paths the from first mask which pass\n    through the second and vice-versa  i.e. only paths\n    which pass through both masks are retained.\n\n waypoints\n    Input is a binary volume for seed mask (-x)\n    also requires a binary waypoint mask or ascii list\n    of waypoint masks (--mask2)\n    (requires a matrix taking both seeds to DTI space (--xfm))\n    Output is a volume containing all the paths from the\n    seedmask which pass through ALL of the waypoint masks.\n"<<endl;
     if ( getenv("FSLINFMRIB"))
       matrixmodehelp(); 
  }