Hi Rick,
Thanks for the advice. I don’t think I will run 3dvolreg if I am running 3dAllineate and it is already doing volume registration. However if I decide to use -1Dmatrix_* option with 3dAllienate then I will need to run 3dvolreg?
The following is the script I ran for 2dImReg/3dvolreg. (Note that 3dvolreg couldn’t run because it uses the 2dreg file that wasn’t created for the base.)
foreach run ( series1 )
2dImReg -prefix ${study}.${subject}.${run}.2dreg -dprefix ${study}.${subject}.2DREGLOG.${run} -base 3 -basefile ${study}.${subject}.${run}.aligned+orig -input ${study}.${subject}.${run}.aligned+orig
3dvolreg -clipit -dfile ${study}.${subject}.3dREGLOG.{$run} -prefix ${study}.${subject}.${run}.3dreg -base 3 ${study}.${subject}.{$run}.2dreg+orig
end
foreach run ( series2 series3 series4 )
2dImReg -prefix ${study}.${subject}.${run}.2dreg -dprefix ${study}.${subject}.2DREGLOG.${run} -base 3 -basefile ${study}.${subject}.${base_run}.aligned+orig -input ${study}.${subject}.${run}.aligned+orig
3dvolreg -clipit -dfile ${study}.${subject}.3dREGLOG.{$run} -prefix ${study}.${subject}.${run}.3dreg -base ${study}.${subject}.{$base_run}.2dreg+orig'[3]' ${study}.${subject}.${run}.2dreg+orig
end
Kristen
