Hi Peter,

Thanks so much for your quick response.

I should also mention that the first time I tried the align_epi_anat.py, I was using .nii files. I was getting an error during SkullStripping that would not allow it to finish, and told me to deoblique my dataset. I then tried the 3dWarp -deoblique on my .nii files which gave me the proper .BRIK and .HEAD files that I use on align_epi_anat.py. This results in (what looks to me) like a proper registration, but I was just worried about the +tlrc suffix.

Also, when I tried 3dcopy to convert my raw .nii file to AFNI format without deobliquing, align_epi_anat.py spits out a brain that is way off from what I want.

I was really just worried 3dWarp and align_epi_anat were automatically warping to some template space, given the +tlrc suffix. Unless there is something else I am missing...?

To answer your questions:

1) My original command is:
$ align_epi_anat.py -anat T1W_anatfile -epi T2W_anatfile -epi_base 0 -cost lpa


2) The output for the afni_system_check.py -check_all is as follows:
=========== afni_system_check.py version 0.5, August 26, 2013 ============

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-504.3.3.el6.x86_64
version: #1 SMP Wed Dec 17 01:55:02 UTC 2014
distribution: CentOS 6.4 Final
number of CPUs: 12
apparent login shell: bash

--------------------- AFNI and related program tests ---------------------
which afni : /project/iconic/apps/afni/AFNI_2011_12_21_1014/install/afni
afni version : Precompiled binary linux_xorg7_64: Dec 19 2013
which python : /usr/bin/python
python version : 2.6.6
which R : /usr/local/bin/R
R version : R version 2.15.3 (2013-03-01) -- "Security Blanket"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/project/iconic/apps/afni/AFNI_2011_12_21_1014/install/afni)
R : 1 (/usr/local/IT/R-2.15.3/bin/R)
python : 1 (/usr/bin/python)

testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success

------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib64/python2.6/site-packages/PyQt4
++ module loaded: PyQt4

------------------------------- path vars --------------------------------
PATH = /project/iconic/apps/afni/AFNI_2011_12_21_1014/install:/usr/local/apps/pgi-13.5/bin:/usr/java/default/jre/bin:/usr/java/default/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr3/graduate/rnauer/bin

PYTHONPATH =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =



-Rachel