Hi Bob,

I tried as you said (with my own program since I am working in bash). Even with as few as 5 TR, it still gets killed.
I also tried with autobox first to try to reduce the size of the EPI. Result was ++ Auto bbox: x=16..60 y=5..65 z=0..33

Result of the 3dNwarpApply was

++ 3dNwarpApply: AFNI version=AFNI_16.3.08 (Nov 4 2016) [64-bit]
++ Authored by: Zhark the Warped
++ opened source dataset 'pb02.HC_S750.r01.tshift+orig[0..5]'
++ output grid size = 3.5 mm
++ -master dataset is '/home/user/abin/MNI152_T1_2009c+tlrc.'
++ Processing -nwarp ++ Enter IW3D_read_nwarp_catlist( ../../group.anat/HC_S750.results/anat.HC_S750.nsFS2_WARP+tlrc whole_matrix_volreg_epi2anat.aff12.1D{0..5} )
+ Open dataset warp ../../group.anat/HC_S750.results/anat.HC_S750.nsFS2_WARP+tlrc
+ max displacments = 200.448 66.7855 129.967
+ Open matrix file whole_matrix_volreg_epi2anat.aff12.1D{0..5}
+ max shifts = 3.84855 0.260578 11.6008
+ --- Totalized max displacments = 204.297 67.0461 141.568
++ IW3D_set_geometry_nwarp_catlist: padding = 204
+ results: master_geomstring = MATRIX(-1,0,0,258,0,-1,0,294,0,0,1,-258):517,554,527 actual_geomstring = MATRIX(-1,0,0,462,0,-1,0,498,0,0,1,-462):925,962,935
+ -- warp #0 geometry = MATRIX(-1,0,0,258,0,-1,0,294,0,0,1,-258):517,554,527
+ regridding warp #0 to geometry = MATRIX(-1,0,0,462,0,-1,0,498,0,0,1,-462):925,962,935
/media/sf_shared_folder/TOOLS-bash//fMRI_preprocessing_newBlur_noDeoblique.sh: line 433: 15804 Killed 3dNwarpApply -verb -nwarp "$anat_warp whole_matrix_volreg_epi2anat.aff12.1D{$start..$end}" -source pb02.$subj.r01.tshift+orig[$start..$end] -dxyz 3.5 -prefix rm.epi.nomask_$i -master ~/abin/MNI152_T1_2009c+tlrc.


The number before the word "Killed" is never the same. But it is always while "regridding warp"

Maybe the problem is not the epi. Do you have any idea why the anat_warp is no much bigger, even if the size of the anat is the same as before?