Hi everybody,

I'm playing around with the afni_proc.py (from Precompiled binary linux_openmp_64: Feb 19 2015 (Version AFNI_2011_12_21_1014)) script for the first time.

I've run it as follows:

subj=330_AA
task=mid

cd ../data/$subj

afni_proc.py \
-subj_id $subj \
-script proc.$subj -scr_overwrite \
-do_block align tlrc \
-copy_anat $subj.anat+orig.HEAD \
-tcat_remove_first_trs 0 \
-dsets ${subj}.${task}?+orig.HEAD \
-align_opts_aea -cost lpa \
-volreg_tlrc_warp \
-volreg_align_to first \
-volreg_align_e2a \
-tlrc_NL_warp \
-tlrc_base MNI_caez_N27+tlrc \
-tlrc_NL_awpy_rm no \
-blur_size 4.2 \
-regress_3dD_stop \
-regress_reml_exec \
-regress_polort 2 \
-regress_censor_motion 0.5 \
-regress_censor_outliers 0.1 \
-regress_bandpass 0.008 0.1 \
-regress_apply_mot_types demean deriv \
-regress_compute_fitts \
-regress_est_blur_epits \
-regress_est_blur_errts

When I run the script it completes until auto_warp.py is invoked and thern terminates prematurely with the following error:

#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_pb01.330_AA.r01.tshift*
#Script is running:
\rm -f ./__tt_330_AA.anat*

# Finished alignment successfully

#++ auto_warp.py version: 0.02
# Output directory /data/sanDiego/r01_preliminary/data/330_AA/330_AA.results/awpy/
#Script is running:
mkdir /data/sanDiego/r01_preliminary/data/330_AA/330_AA.results/awpy/
cd /data/sanDiego/r01_preliminary/data/330_AA/330_AA.results/awpy/
#Script is running (command trimmed):
3dcopy /data/sanDiego/r01_preliminary/data/330_AA/330_AA.results/330_AA.anat_ns+orig ./anat.nii
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
** ERROR: Could not strip skull

** ERROR - script failed
** missing +tlrc warp dataset: 330_AA.anat_ns+tlrc.HEAD

Is the inability to handle compressed nii files a error on the part of auto_warp.py or 3dUnifize? (I also have AFNI_COMPRESSOR=GZIP in my environment.)



Edited 1 time(s). Last edit at 02/26/2015 03:44PM by Colm Connolly.