Hi,
I experienced a failure while running align_epi_anat.py; the screen output follows this message. The problem seems to be with the version of 3dvolreg that the script ran, specifically with the -1Dmatrix_save flag. However, I don't think our 3dvolreg should be out of date--we just installed the latest Linux xorg7 64bit package from the AFNI website, and
> which 3dvolreg
returns the path to this latest installation. Please let me know if you can make sense of this.
Thanks,
Jeff
#++ align_epi_anat version: 1.17
#Script is running (command trimmed):
3dAttribute DELTA 0004+orig
#++ Spacing for EPI to tlrc alignment is 3.750000 mm
#Script is running (command trimmed):
3dAttribute DELTA 121908.mprage+orig
#++ Spacing for anat to EPI deobliquing is 1.000000 mm
#++ Removing all the temporary files
#Script is running:
rm -f __tt_0004*
#Script is running:
rm -f __tt_121908.mprage*
#Script is running (command trimmed):
3dcopy 121908.mprage+orig __tt_121908.mprage
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Jan 5 2009) [64-bit]
#++ Removing skull from anatomical data
#Script is running (command trimmed):
3dSkullStrip -input __tt_121908.mprage+orig -prefix __tt_121908.mprage_ns
The intensity in the output dataset is a modified version
of the intensity in the input volume.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
3dcalc -a __tt_121908.mprage+orig -b __tt_121908.mprage_ns+orig -expr 'a*step(b)' \
-prefix __tt_121908.mprage_ns_orig_vol
to generate a new masked version of the input.
#Script is running (command trimmed):
3dinfo __tt_121908.mprage_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /data/projects/32ch_121908/121908-2/rawdata/sortedDICOMs/121908-17/__tt_121908.mprage_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo 0004+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /data/projects/32ch_121908/121908-2/rawdata/sortedDICOMs/121908-17/0004+orig is not oblique
#Script is running (command trimmed):
3dAttribute TAXIS_OFFSETS 0004+orig
#++ Correcting for slice timing
#Script is running (command trimmed):
3dTshift -prefix __tt_0004_tsh -cubic 0004+orig
++ 3dTshift: AFNI version=AFNI_2008_07_18_1710 (Jan 5 2009) [64-bit]
#++ Volume registration for epi data
#Script is running (command trimmed):
3dvolreg -1Dfile __tt_0004_tsh_vr_motion.1D -1Dmatrix_save __tt_0004_tsh_vr_mat.aff12.1D -prefix __tt_0004_tsh_vr -base 5 -cubic __tt_0004_tsh+orig
++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [64-bit]
++ Authored by: RW Cox
** Unknown option: -1Dmatrix_save
#**ERROR Could not do volume registration
Traceback (most recent call last):
File "/usr/bin/AFNI/align_epi_anat.py", line 2384, in ?
ps.epi_ts, ps.epi_vr, ps.epi_ns = \
File "/usr/bin/AFNI/align_epi_anat.py", line 2119, in process_epi
o = self.tstat_epi(o, ps.tstat_opt, prefix)
File "/usr/bin/AFNI/align_epi_anat.py", line 1632, in tstat_epi
o = e.new(prefix)
AttributeError: 'NoneType' object has no attribute 'new'
[jeffreyp@thinking 121908-17]$
++ VERSION CHECK! This program = AFNI_2006_03_21_1314
++ Current AFNI website = AFNI_2008_07_18_1710
