Hi everybody,

I'm having trouble getting 3dAllineate (called via align_epi_anat.py) to complete: it's continually terminating with an Abort.

I call align_epi_anat.py as follows

align_epi_anat.py -anat 330_A.anat_struc_brain.std+orig.HEAD -anat_has_skull no -epi_strip 3dAutomask -epi 330_A.restingstate.std+orig.HEAD -epi_base 0 -epi2anat

which does it's thing and then calls 3dAllineate yielding

#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix __tt_330_A.anat_struc_brain.std_al_wtal -weight ./__tt_330_A.restingstate.std_vr_ts_rs_ns_wt+orig -source ./__tt_330_A.anat_struc_brain.std+orig -prefix __tt_330_A.anat_struc_brain.std_al -base ./__tt_330_A.restingstate.std_vr_ts_rs_ns+orig -nocmass -1Dmatrix_save 330_A.anat_struc_brain.std_al_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (Jul 8 2012) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_330_A.anat_struc_brain.std+orig.HEAD
++ Base dataset: ./__tt_330_A.restingstate.std_vr_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1637954 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1371970 voxels [12.5%] in weight mask
++ Number of points for matching = 1371970
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -53.6..53.6 -81.9..81.9 -81.9..81.9
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ OpenMP thread count = 2
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== sub-brick #0 ========== [total CPU to here=13.5 s]
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - copying weight image
+ - using 1371970 points from base image [use_all=0]
+ * Exit alignment setup routine
+ 1293166 total points stored in 2428 'RHDD(6.54321)' bloks
+ - Initial cost = -0.203466
+ - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
*************************************************************************************
+ - Finalish cost = -0.692747 ; 243 funcs
Abort

The remainder of the a_e_a.py fails from this point on.

I'm at a loss as to the cause of the Abort as there is no core file dumped from which to get a backtrace.

Im running MAC OS X 10.7 with afni -ver
Version AFNI_2011_12_21_1014
[[Precompiled binary macosx_10.6_Intel_64: Jul 8 2012]]

To make matters worse this problem is intermittent: I've just got the command to complete, but by and large it fails.

Any idea what might be causign this problem. I's been plaguing me since last week.

Thanks.

Colm.



Edited 1 time(s). Last edit at 07/09/2012 06:01PM by Colm Connolly.