1) After updating, I still get the error
Traceback (most recent call last):
File "/Users/lguo15/abin/afni_proc.py", line 2690, in <module>
rv = run_proc()
File "/Users/lguo15/abin/afni_proc.py", line 2676, in run_proc
rv = ps.create_script()
File "/Users/lguo15/abin/afni_proc.py", line 1647, in create_script
self.make_exec()
File "/Users/lguo15/abin/afni_proc.py", line 2246, in make_exec
os.chmod(self.script, 0755)
OSError: [Errno 13] Permission denied: 'proc.p43'

2) I do have enough space and here is the output
Filesystem Size Used Avail Capacity iused ifree %iused Mounted on
/dev/disk2 2.8Ti 52Gi 2.8Ti 2% 13677829 746874809 2% /
devfs 186Ki 186Ki 0Bi 100% 644 0 100% /dev
map -hosts 0Bi 0Bi 0Bi 100% 0 0 100% /net
map auto_home 0Bi 0Bi 0Bi 100% 0 0 100% /home
map -fstab 0Bi 0Bi 0Bi 100% 0 0 100% /Network/Servers
[server address] 16Ti 10Ti 5.9Ti 64% 2711449666 1583484849 63% /Volumes/server

3) here is the output for ls -al in the individual data folder for which I was trying to generate a preprocessing script.
total 1548008
drwx------+ 1 lguo15 WIN\Domain Users 16384 Dec 1 13:56 .
drwx------+ 1 lguo15 WIN\Domain Users 16384 Nov 15 17:18 ..
-rwx------+ 1 lguo15 WIN\Domain Users 6148 Dec 1 13:54 .DS_Store
-rwx------+ 1 lguo15 WIN\Domain Users 322 Nov 23 14:46 .profile
-rwx------+ 1 lguo15 WIN\Domain Users 126784000 May 22 2015 WM_run1+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 16476 May 22 2015 WM_run1+orig.HEAD
-rwx------+ 1 lguo15 WIN\Domain Users 126784000 May 22 2015 WM_run2+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 16476 May 22 2015 WM_run2+orig.HEAD
-rwx------+ 1 lguo15 WIN\Domain Users 126784000 May 22 2015 WM_run3+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 16476 May 22 2015 WM_run3+orig.HEAD
-rwx------+ 1 lguo15 WIN\Domain Users 126784000 May 22 2015 WM_run4+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 16477 May 22 2015 WM_run4+orig.HEAD
-rwx------+ 1 lguo15 WIN\Domain Users 126784000 May 22 2015 WM_run5+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 16477 May 22 2015 WM_run5+orig.HEAD
drwx------@ 1 lguo15 WIN\Domain Users 16384 May 25 2015 fs
-rwx------+ 1 lguo15 WIN\Domain Users 13545 Nov 23 16:52 preproc.p43
-rwx------+ 1 lguo15 WIN\Domain Users 71680000 May 22 2015 quadlocal_run1+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 10616 May 22 2015 quadlocal_run1+orig.HEAD
-rwx------+ 1 lguo15 WIN\Domain Users 71680000 May 22 2015 quadlocal_run2+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 10616 May 22 2015 quadlocal_run2+orig.HEAD
drwx------+ 1 lguo15 WIN\Domain Users 16384 May 22 2015 raw
-rwx------+ 1 lguo15 WIN\Domain Users 15052800 May 22 2015 struct+orig.BRIK
-rwx------+ 1 lguo15 WIN\Domain Users 5543 May 22 2015 struct+orig.HEAD

4) This is the output for csrutil status
csrutil status
System Integrity Protection status: enabled (Custom Configuration).

Configuration:
Apple Internal: disabled
Kext Signing: disabled
Filesystem Protections: disabled
Debugging Restrictions: disabled
DTrace Restrictions: disabled
NVRAM Protections: disabled

This is an unsupported configuration, likely to break in the future and leave your machine in an unknown state.

5) I am not sure how to do chmod 775 on mac...

6) I checked the disk utility and ran First Aid which did not identify any problems with permissions.