AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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fengfeng
February 24, 2015 04:21AM
Dear all,
I am trying to use the matlab package PESTICA, which is closely associated with AFNI, 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
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Subject Author Posted

PESTICA: option to change data directory and orientation

fengfeng February 24, 2015 04:21AM

Re: PESTICA: option to change data directory and orientation

Daniel Glen February 24, 2015 07:07AM

Re: PESTICA: option to change data directory and orientation

fengfeng February 24, 2015 09:44PM