HI,

I'm fairly new to AFNI, and i've been trying to figure out how to streamline processing subjects via afni_proc.py (and uber_subject.py). I was able to generate a shell script for one subject, but when I altered this script I was unable to run my script again. (I'm currently just focusing on preprocessing atm)

An Example would be:

********************************************************************************************************************************************
#!/usr/bin/env tcsh

# created by uber_subject.py: version 0.36 (April 5, 2013)
# creation date: Wed Feb 11 17:32:06 2015

# set data directories
set top_dir = \
/Users/debbieyee/Documents/Classes/2015_Spring/fMRI/Data/HCPPILOTDATA/CP10023

# set subject and group identifiers
set subj = CP10023
set group_id = HCPPILOTDATA

# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj \
-script proc.GAMBER.$subj -scr_overwrite \
-out_dir $subj.GAMBER \
-dsets \
$top_dir/BOLDGAMBER1.nii.gz \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $top_dir/MPRAGE.nii.gz \
-anat_has_skull yes \
-tcat_remove_first_trs 0 \
-tshift_opts_ts -tpattern alt+z2 \
-align_opts_aea -giant_move \
-volreg_align_to first \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 4.0 \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-move_preproc_files

********************************************************************************************************************************************

I tried executiing this again once I've changed the "subj" variable, but I'm running into an error that keeps telling me that -subj_id requires 1 params, but finds 0. I clearly have a subject ID in my script, but I'm unsure of why I continue to get this error. The error is shown below:

********************************************************************************************************************************************
[Debbies-MacBook-Pro:subject_results/group.HCPPILOTDATA/subj.CP10023] debbieyee% sh cmd.ap.CP10023
** error: arg #1 (-subj_id) requires 1 params, found 0
----------------------------------------------------------------------
** failed command (get_user_opts):

afni_proc.py -subj_id -script proc.GAMBER. -scr_overwrite -out_dir .GAMBER \
-dsets /BOLDGAMBER1.nii.gz -blocks tshift align tlrc volreg blur mask \
scale regress -copy_anat /MPRAGE.nii.gz -anat_has_skull yes \
-tcat_remove_first_trs 0 -tshift_opts_ts -tpattern alt+z2 \
-align_opts_aea -giant_move -volreg_align_to first -volreg_align_e2a \
-volreg_tlrc_warp -blur_size 4.0 -regress_motion_per_run \
-regress_censor_motion 0.3 -regress_est_blur_epits \
-regress_est_blur_errts -move_preproc_files
----------------------------------------------------------------------

********************************************************************************************************************************************

If anyone has run into this issue, or might have any suggestions on how to debug, I would appreciate it. I'm not quite sure what to do next, given that I've tried updating the afni binaries, trying uber_subject.py on the same subject, changing permissions (its not a an execution problem), etc. Not sure what to do next -- any help or advice would be appreciated.

Thanks,
Debbie



Edited 2 time(s). Last edit at 02/11/2015 07:00PM by debyee.