Thank you for the clarification! I will subscript to the email list so I am up to date with AFNI software.
When I run afni -ver I get the following output:
Precompiled binary linux_ubuntu_16_64: Apr 30 2018 (Version AFNI_18.1.09)
My afni_proc.py script is:
# script generated by the command:
#
# afni_proc.py -subj_id SSwarp_proc_9409_aug30 -script SSwarp_proc_9409_aug30 \
# -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress \
# -copy_anat \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/anatSS.MNI152_2009_template_SSW.nii.gz.nii \
# -dsets /home/bmiadmin/Tamara/PRR_Analysis/9409/9409.1+orig.HEAD \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/9409.2+orig.HEAD \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/9409.3+orig.HEAD \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/9409.4+orig.HEAD \
# -anat_has_skull no -tcat_remove_first_trs 0 -volreg_align_to last \
# -volreg_align_e2a -volreg_tlrc_warp -tlrc_base \
# MNI152_2009_template_SSW.nii -tlrc_NL_warp -tlrc_NL_warped_dsets \
# anatQQ.MNI152_2009_template_SSW.nii.gz.nii \
# anatQQ.MNI152_2009_template_SSW.nii.gz.aff12.1D \
# anatQQ.MNI152_2009_template_SSW.nii.gz_WARP.nii -blur_size 4.0 \
# -regress_stim_times \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_corr_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_corr.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_incor_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_incor.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_corr_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_corr.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_incor_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_incor.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_corr_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_corr.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_incor_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_incor.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_corr_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_corr.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_incor_fed.txt \
# /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_incor.txt \
# -regress_stim_labels NonRevP_learn_corr_fed NonRevP_learn_corr \
# NonRevP_learn_incor_fed NonRevP_learn_incor NonRevP_perf_corr_fed \
# NonRevP_perf_corr NonRevP_perf_incor_fed NonRevP_perf_incor \
# RevP_acq_corr_fed RevP_acq_corr RevP_acq_incor_fed RevP_acq_incor \
# RevP_rev_corr_fed RevP_rev_corr RevP_rev_incor_fed RevP_rev_incor \
# -regress_basis dmBLOCK -regress_stim_types AM1 -regress_censor_motion \
# 2.0 -regress_censor_outliers 0.1 -regress_apply_mot_types demean deriv \
# -regress_motion_per_run -regress_make_ideal_sum sum_ideal.1D \
# -regress_est_blur_epits -regress_est_blur_errts -regress_run_clustsim no
The Error Message in the terminal:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/bmiadmin/subjects
MNI_DIR /usr/local/freesurfer/mni
SUBJECTS_DIR= /home/bmiadmin/subjects
mitchelllab-linux:~/Tamara/PRR_Analysis/9409> tcsh -xef SSwarp_proc_9409_aug30 |& tee output.SSwarp_proc_9409_aug30
echo auto-generated by afni_proc.py, Thu Aug 30 09:45:30 2018
auto-generated by afni_proc.py, Thu Aug 30 09:45:30 2018
echo (version 6.10, Apr 26, 2018)
(version 6.10, Apr 26, 2018)
echo execution started: `date`
date
execution started: Thu Aug 30 09:55:40 EDT 2018
afni -ver
Precompiled binary linux_ubuntu_16_64: Apr 30 2018 (Version AFNI_18.1.09)
afni_history -check_date 23 Mar 2018
-- is current: afni_history as new as: 23 Mar 2018
most recent entry is: 29 Apr 2018
if ( 0 ) then
if ( 0 > 0 ) then
set subj = SSwarp_proc_9409_aug30
endif
set output_dir = SSwarp_proc_9409_aug30.results
if ( -d SSwarp_proc_9409_aug30.results ) then
set runs = ( `count -digits 2 1 4` )
count -digits 2 1 4
mkdir SSwarp_proc_9409_aug30.results
mkdir SSwarp_proc_9409_aug30.results/stimuli
cp /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_incor.txt SSwarp_proc_9409_aug30.results/stimuli
3dcopy anatSS.MNI152_2009_template_SSW.nii.gz.nii SSwarp_proc_9409_aug30.results/anatSS.MNI152_2009_template_SSW.nii.gz
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dcopy anatQQ.MNI152_2009_template_SSW.nii.gz.nii SSwarp_proc_9409_aug30.results/anatQQ.MNI152_2009_template_SSW.nii.gz
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dcopy anatQQ.MNI152_2009_template_SSW.nii.gz.aff12.1D SSwarp_proc_9409_aug30.results/anatQQ.MNI152_2009_template_SSW.nii.gz.aff12.1D
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dcopy anatQQ.MNI152_2009_template_SSW.nii.gz_WARP.nii SSwarp_proc_9409_aug30.results/anatQQ.MNI152_2009_template_SSW.nii.gz_WARP.nii
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dTcat -prefix SSwarp_proc_9409_aug30.results/pb00.SSwarp_proc_9409_aug30.r01.tcat 9409.1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.2 s
3dTcat -prefix SSwarp_proc_9409_aug30.results/pb00.SSwarp_proc_9409_aug30.r02.tcat 9409.2+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.2 s
3dTcat -prefix SSwarp_proc_9409_aug30.results/pb00.SSwarp_proc_9409_aug30.r03.tcat 9409.3+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.2 s
3dTcat -prefix SSwarp_proc_9409_aug30.results/pb00.SSwarp_proc_9409_aug30.r04.tcat 9409.4+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.2 s
set tr_counts = ( 153 153 153 153 )
cd SSwarp_proc_9409_aug30.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 04 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.SSwarp_proc_9409_aug30.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r01.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 107968 voxels passed mask/clip
1deval -a outcount.r01.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.SSwarp_proc_9409_aug30.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r02.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 108219 voxels passed mask/clip
1deval -a outcount.r02.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.SSwarp_proc_9409_aug30.r03.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r03.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 108215 voxels passed mask/clip
1deval -a outcount.r03.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.SSwarp_proc_9409_aug30.r04.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r04.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 107669 voxels passed mask/clip
1deval -a outcount.r04.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r04.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D outcount.r04.1D
cat rm.out.cen.r01.1D rm.out.cen.r02.1D rm.out.cen.r03.1D rm.out.cen.r04.1D
foreach run ( 01 02 03 04 )
3dTshift -tzero 0 -quintic -prefix pb01.SSwarp_proc_9409_aug30.r01.tshift pb00.SSwarp_proc_9409_aug30.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r01.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.SSwarp_proc_9409_aug30.r02.tshift pb00.SSwarp_proc_9409_aug30.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r02.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.SSwarp_proc_9409_aug30.r03.tshift pb00.SSwarp_proc_9409_aug30.r03.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r03.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.SSwarp_proc_9409_aug30.r04.tshift pb00.SSwarp_proc_9409_aug30.r04.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.SSwarp_proc_9409_aug30.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.SSwarp_proc_9409_aug30.r04.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dbucket -prefix vr_base pb01.SSwarp_proc_9409_aug30.r04.tshift+orig[152]
++ 3dbucket: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
align_epi_anat.py -anat2epi -anat anatSS.MNI152_2009_template_SSW.nii.gz+orig -suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask -anat_has_skull no -volreg off -tshift off
#++ align_epi_anat version: 1.58
#++ turning off volume registration
** ERROR: Could not find anat / dset1 dataset
/home/bmiadmin/Tamara/PRR_Analysis/9409/SSwarp_proc_9409_aug30.results/anatSS.MNI152_2009_template_SSW.nii.gz+orig
** ERROR - script failed
mitchelllab-linux:~/Tamara/PRR_Analysis/9409>
