Dear all,
I am trying to use the matlab package PESTICA to correct for potential influence of physiological noise. I downloaded the package "pestica_afni_v2" from [www.nitrc.org]. Firstly, I tried to modify parameter settings in the setup_pestica.sh according to the tutorial, e.g., voxel volume and MATLAB and afni_matlab setup. However, I couldn't find the option to change data directory and orientation. Secondly, I ran setup_pestica.sh anyway. Thirdly, in my data directory, I ran run_pestica.sh -d data step by step from 1 to 6 smoothly! I am still wondering whether data directory and orientation setup are necessary.
Another question related to setup_pestica.sh: after performing "source setup_pestica.sh", I checked environment variable setting by "env | grep pestica" and only got PESTICA_DIR, without showing "PESTICA_ORIENT", "PESTICA_VOL" or "PESTICA_SLICE_TIMING". Anyone has suggestions?
Thanks,
Qihong

Please note, Qihong and I have been discussing off-line. We are now talking about denoising 3D data, and I'm recommending that PESTICA is unlikely to work for 3D acquisitions. FSL Melodic may be the only "accepted" method, but please note that spatial whole-brain ICA does NOT remove physiologic noise anywhere near as well as a model-based regression using either pulse/resp or PESTICA (see http://www.ncbi.nlm.nih.gov/pubmed/20600... for a very careful evaluation of Infomax and FastICA in spatial whole-brain ICA at removing physio noise).

Erik