Getting closer, I think. The warp now shows up in the 3dAllineate command, but there is a fatal error in there.

thanks!

doug

align_epi_anat.py -epi2anat -anat_has_skull no -Allineate_opts "-weight_frac 1.0 -maxrot 45 -maxshf 40 -VERB -warp shift_rotate" -big_move -cmass cmass -anat refvol.lpcreg+orig -epi movvol.lpcreg+orig -epi_base 0
#++ align_epi_anat version: 1.19
#Script is running (command trimmed):
3dAttribute DELTA movvol.lpcreg+orig
#++ Spacing for EPI to tlrc alignment is 3.437500 mm
#Script is running (command trimmed):
3dAttribute DELTA refvol.lpcreg+orig
#++ Spacing for anat to EPI deobliquing is 1.000000 mm
#++ Removing all the temporary files
#Script is running:
rm -f __tt_movvol.lpcreg*
#Script is running:
rm -f __tt_refvol.lpcreg*
#Script is running (command trimmed):
3dcopy refvol.lpcreg+orig __tt_refvol.lpcreg
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (May 8 2009) [64-bit]
#Script is running (command trimmed):
3dinfo __tt_refvol.lpcreg+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /autofs/space/crash_001/users/greve/lpc/tmp.lpc06/__tt_refvol.lpcreg+orig is not oblique
#Script is running (command trimmed):
3dinfo movvol.lpcreg+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /autofs/space/crash_001/users/greve/lpc/tmp.lpc06/movvol.lpcreg+orig is ***oblique****
#++ Matching obliquity of anat to epi
#++ Matching obliquity of anat to epi
#Script is running (command trimmed):
3dWarp -verb -card2oblique movvol.lpcreg+orig -prefix __tt_refvol.lpcreg_ob -newgrid 1.000000 __tt_refvol.lpcreg+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > __tt_refvol.lpcreg_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_2008_07_18_1710 (May 8 2009) [64-bit]
++ Authored by: RW Cox
++ Output dataset ./__tt_refvol.lpcreg_ob+orig.BRIK
#Script is running (command trimmed):
3dAttribute TAXIS_OFFSETS movvol.lpcreg+orig
#++ Can not do time shifting of slices. Data is already time shifted
#++ Skipping time series volume registration. Must have more than a single sub-brick.
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix __tt_movvol.lpcreg_ts movvol.lpcreg+orig'[0]'
++ 3dbucket: AFNI version=AFNI_2008_07_18_1710 (May 8 2009) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./movvol.lpcreg+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:./movvol.lpcreg+orig.BRIK is 13.100002 degrees from plumb.
#++ resampling epi to match anatomical data
#Script is running (command trimmed):
3dresample -master __tt_refvol.lpcreg_ob+orig -prefix __tt_movvol.lpcreg_ts_rs -inset __tt_movvol.lpcreg_ts+orig'' -rmode Cu
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_movvol.lpcreg_ts+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:./__tt_movvol.lpcreg_ts+orig.BRIK is 13.100002 degrees from plumb.
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -input __tt_movvol.lpcreg_ts_rs+orig -prefix __tt_movvol.lpcreg_ts_rs_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_movvol.lpcreg_ts_rs+orig -b __tt_movvol.lpcreg_ts_rs_ns+orig -expr 'a*step(b)' \
-prefix __tt_movvol.lpcreg_ts_rs_ns_orig_vol
to generate a new masked version of the input.
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 __tt_movvol.lpcreg_ts_rs_ns+orig
#++ Applying threshold of 3193.000000 on /autofs/space/crash_001/users/greve/lpc/tmp.lpc06/__tt_movvol.lpcreg_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix __tt_movvol.lpcreg_ts_rs_ns_wt -a __tt_movvol.lpcreg_ts_rs_ns+orig -expr 'min(1,(a/3193.000000))'
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (May 8 2009) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__tt_movvol.lpcreg_ts_rs_ns_wt+orig.BRIK
#++ Aligning anatomical data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix __tt_refvol.lpcreg_ob_al_wtal -weight __tt_movvol.lpcreg_ts_rs_ns_wt+orig -source __tt_refvol.lpcreg_ob+orig -prefix __tt_refvol.lpcreg_ob_temp_al -base __tt_movvol.lpcreg_ts_rs_ns+orig -cmass -1Dmatrix_save refvol.lpcreg_al_e2a_only_mat.aff12.1D -master SOURCE "-weight_frac 1.0 -maxrot 45 -maxshf 40 -VERB -warp shift_rotate" -twopass
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (May 8 2009) [64-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
++ Zero-pad: not needed
++ 1547969 voxels [6.4%] in weight mask
++ Output dataset ./__tt_refvol.lpcreg_ob_al_wtal+orig.BRIK
++ Number of points for matching = 0
++ Local correlation: blok type = 'RHDD(6.54321)'
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== sub-brick #0 ========== [total CPU=1.7 s]
++ Start coarse pass
+ - Search for coarse starting parameters
++ *** Fine pass begins ***

Fatal Signal 11 (SIGSEGV) received
GA_scalar_costfun
GA_scalar_fitter
mri_genalign_scalar_cost
3dAllineate
Bottom of Debug Stack
** AFNI version = AFNI_2008_07_18_1710 Compile date = May 8 2009
** [[Precompiled binary linux_gcc33_64: May 8 2009]]
** Program Abort **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
#Script is running:
cat_matvec -ONELINE refvol.lpcreg_al_e2a_only_mat.aff12.1D __tt_refvol.lpcreg_obla2e_mat.1D -I > refvol.lpcreg_al_mat.aff12.1D
** FATAL ERROR: Can't read file 'refvol.lpcreg_al_e2a_only_mat.aff12.1D'
** Program compile date = May 8 2009
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base __tt_movvol.lpcreg_ts_rs_ns+orig -1Dmatrix_apply refvol.lpcreg_al_mat.aff12.1D -prefix refvol.lpcreg_al -input __tt_refvol.lpcreg+orig -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (May 8 2009) [64-bit]
++ Authored by: Emperor Zhark
** FATAL ERROR: Can't read -1Dmatrix_apply 'refvol.lpcreg_al_mat.aff12.1D'
** Program compile date = May 8 2009
#**ERROR Could not square a circle (3dAllineate could not align anat to epi)
Traceback (most recent call last):
File "/autofs/space/crash_001/users/greve/afni/linux_gcc33_64/align_epi_anat.py", line 2459, in ?
ps.anat_alnd, ps.anat_alndwt = \
TypeError: unpack non-sequence