Thanks for your prompt and detailed response. As far as spatial filtering is concerned, in both of these cases, I have applied spatial smoothing with FWHM of 3mm, and that I have done during ICA Aroma (temporal filtering turned OFF). For temporal filtering, for one of them, I used Feat gui (with all other options including spatial filtering turned OFF and a cutoff period of 50s) and for the other, I used fslmaths command (with sigma = 50 / 2 *TR). I was expecting to see the same filtered-output (in fslview) in both of these cases.
"Are you sure that you are selecting the correct settings for what you want?" If what you are asking is, if I am setting everything correctly in the Feat gui, then you can see a demo design fsf file that I am attaching with this email. It is HPF with everything else turned OFF.
Also, I tried to search for a similar command in feat report logs, it looks it does this multistage filtering with a few intermediary files like prefiltered_func_data.
/opt/fsl/fsl-5.0.9/fsl/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_thresh
/opt/fsl/fsl-5.0.9/fsl/bin/fslmaths prefiltered_func_data_thresh -mul 1.02946522499 prefiltered_func_data_intnorm
/opt/fsl/fsl-5.0.9/fsl/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean
/opt/fsl/fsl-5.0.9/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 29.4117647059 -1 -add tempMean prefiltered_func_data_tempfilt