Having read through several threads on the message board I am puzzled as to when I should use 3dmerge to spatially smooth my data.
Currently I am implementing the following preprocessing steps in the order given:
1. Clipping the data using 3dAutomask and 3dcalc
2. Motion correcting the data using 3dvolreg
3. Linear Detrending using 3dTcat -rlt+
4. Spatial Blurring using 3dmerge -1blur fwhm 5 (original vox. res. 2.5mm)
5. Temporal Smoothing using 3dTsmooth
6. High Pass Filtering using 3dFourier at .02 Hz -retrend
7. Normalizing to Percent Change using 3dcalc

Should spatial blurring be the last step or in general does thi seem like a logical order to proceed with preprocessing.

Another question I have is before high pass filtering the data the signal for a given slice will be relatively stable over time, however after filtering there is a general trend for the singal level to decrease over time. Is this an artificat of filtering as a last step or the use of the -retrend option. If HP filtering last should I use the -retrend option?