Hi Folks,

PESTICA processes could increase the background intensity, and there might be a trouble to perform further processes (i.e. getting a wrong brain mask from the output irfretroicor file during afni_proc.py process).

Few AFNI command lines can correct the background intensity problem:

# pick the time course intensities at voxel index 1 1 1
3dmaskdump -quiet -noijk -ibox 1 1 1 [output irfretroicor file here]+orig. > temp.1D
# sort the intensities
1dTsort temp.1D\' > tempsort.1D

# For tcsh, get the minimum number of background, but mostly identical to each other.
set mm = '1dcat tempsort.1D'{0}''

# subtract the minimum background intensity across time points
3dcalc -a pb01.irfretroicor+orig. -expr 'a-'${mm}'' -prefix irfretroicor_bg_fix

I hope this helps.

H