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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Peter Molfese
July 06, 2015 01:29PM
It looks like the shell isn't reading your entire afni_proc.py command for whatever reason. You can see that the generated script says what call it received. It happens to cut off when it hits the first commented out (#-copy_anat ${subfolder}/${subject}/p*/e*/${subject}.${study}.spgr+orig \) line in your script. 

# script generated by the command: 
# 
# afni_proc.py -subj_id sub11 -script \ 
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Scripts/Imagery/sub11_imagery_proc_script \ 
# -out_dir \ 
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.imagery.results \ 
# -dsets \ 
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Neutral+orig.HEAD \ 
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/sub11.PTSD_Conditioning.Trauma+orig.HEAD \ 
# -copy_anat \ 
# /media/LarsonDrive/MRI6/PTSD_Conditioning/Subject_Data/sub11/p532/e542/sub11.PTSD_Conditioning.spgr+orig

From here I would suggest you check all of your lines to see if there is a space after any continuation backslash (\). You can also use file_tool: 

file_tool -test -infiles my_scripts_*.txt

Alternatively you can put all of you script into a single line for testing!
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Subject Author Posted

Script is skipping Non-Linear Warping

lindsle6 July 06, 2015 12:22PM

Re: Script is skipping Non-Linear Warping

Peter Molfese July 06, 2015 12:38PM

Re: Script is skipping Non-Linear Warping

lindsle6 July 06, 2015 01:20PM

Re: Script is skipping Non-Linear Warping

Peter Molfese July 06, 2015 01:29PM

Re: Script is skipping Non-Linear Warping

rick reynolds July 06, 2015 02:25PM

Re: Script is skipping Non-Linear Warping

Isaac Schwabacher July 13, 2015 02:38PM

Re: Script is skipping Non-Linear Warping

rick reynolds July 13, 2015 04:20PM

Re: Script is skipping Non-Linear Warping

Isaac Schwabacher July 13, 2015 05:00PM

Re: Script is skipping Non-Linear Warping

rick reynolds July 13, 2015 08:37PM