The final file name in the afni_proc.py

AFNI Message Board
1

afni_proc.py -subj_id $sb
-blocks tshift align tlrc volreg blur mask scale
-copy_anat ${sb}_SurfVol.nii
-dsets
${path_dest}/function/$sb/func1/func1+orig.HEAD
${path_dest}/function/$sb/func2/func2+orig.HEAD
-tcat_remove_first_trs 2
-tlrc_base MNI152_2009_template.nii.gz
-tlrc_NL_warp
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-blur_size 8
-volreg_tlrc_warp

So, which name of file will be the final result that I want?

2

You don’t have a “regress” block? Are you sure that is what you want/don’t want?

–pt

3

Hi
Thanks for your reply. I want to perform PPI analysis. After this afni_proc.py, regression analyses with PPI regressor will be performed in the following script with 3dDeconvolve. This is because I do not know how to set PPI regressor in the afni_proc.py.

4

Hm, I see. Rick will likely be able to address using afni_proc.py with PPI analyses in mind. As your afni_proc.py is written at the moment, I don’t know that the multiple runs would be concatenated at the end; you will might just have two files with names “pbscale”.

But you might want to look at the AFNI Bootcamp demo data set, obtainable for example from the “Boot up” section here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/bootcamp_stuff.html
… and, in particular, in “AFNI_data6/FT_analysis/PPI/” there is a set of scripts+README file for performing PPI, including an afni_proc.py command, a script to generate PPI regressors, and more.

–pt