Finally, after upgrading to AFNI 16.2.17, slicemoco_newalgorithm.sh -d epiFile -r worked with my setup (Ubuntu 14.04 LTS, Matlab R2012b). Thank you for your help so far!

However, I encountered another issue while running second order moco (whole error output below).

You might have an idea what's going wrong especially where it reads:

===
Error in convert_1dmat_into_tranmatarray (line 3)
[zdim tdim veclen] = size(transmat1d_zt);
Output argument "tranmat_zt" (and maybe others) not assigned during call to
"/mrt/Applications/pestica4/slomoco/convert_1dmat_into_tranmatarray.m>convert_1dmat_into_tranmatarray".
Error in slicemoco_newalgorithm_input (line 25)
tranmat_zt = convert_1dmat_into_tranmatarray(transmat1d_zt);% tranmat_zt =
reshape(tranmat_zt,[zmbdim tdim 3 4]); % (v1) debugged
===

Thank you!

Christian





Whole error output during "slicemoco_newalgorithm.sh -d epiFile -r:
===
finished slicewise in-plane motion correction
Exiting

Running Secondorder Motion Correction using SLOMOCO output
cp ../pestica4/card_pestica4.dat card_pestica4.dat
cp ../pestica4/resp_pestica4.dat resp_pestica4.dat
matlab -nojvm -nosplash addpath /mrt/Applications/pestica4/slomoco; addpath /mrt/Applications/pestica4/afni_matlab; addpath /mrt/Applications/pestica4/pestica_matlab; CARD=load('card_pestica4.dat'); RESP=load('resp_pestica4.dat'); slicemoco_newalgorithm_input('OutBrick_run_022.slicemocoxy_afni+orig','OutBrick_run_022.brain+orig','tempslmoco_volslc_alg_vol_OutBrick_run_022.slicemocoxy_afni/motion.wholevol_zt',CARD,RESP); exit;

< M A T L A B (R) >
Copyright 1984-2012 The MathWorks, Inc.
R2012b (8.0.0.783) 64-bit (glnxa64)
August 22, 2012
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit http://www.mathworks.com.

>> Note: SMS acquisition is applied (MB acc. fac = 6).
Error in convert_1dmat_into_tranmatarray (line 3)
[zdim tdim veclen] = size(transmat1d_zt);
Output argument "tranmat_zt" (and maybe others) not assigned during call to
"/mrt/Applications/pestica4/slomoco/convert_1dmat_into_tranmatarray.m>convert_1dmat_into_tranmatarray".
Error in slicemoco_newalgorithm_input (line 25)
tranmat_zt = convert_1dmat_into_tranmatarray(transmat1d_zt);% tranmat_zt =
reshape(tranmat_zt,[zmbdim tdim 3 4]); % (v1) debugged
>> matlab -nojvm -nosplash addpath /mrt/Applications/pestica4/slomoco; addpath /mrt/Applications/pestica4/pestica_matlab; addpath /mrt/Applications/pestica4/afni_matlab; qa_slomoco('OutBrick_run_022.slicemocoxy_afni+orig','tempslmoco_volslc_alg_vol_OutBrick_run_022.slicemocoxy_afni/motion.wholevol_zt','tempslmocoxy_afni_OutBrick_run_022'); exit;

< M A T L A B (R) >
Copyright 1984-2012 The MathWorks, Inc.
R2012b (8.0.0.783) 64-bit (glnxa64)
August 22, 2012
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit http://www.mathworks.com.

>> Note: SMS acquisition is applied (MB acc. fac = 6).
Index exceeds matrix dimensions.
Error in qa_slomoco (line 61)
outofplane(acqtp,:) = rotmat_zt(z,t,:); % [tdim*zmbdim [dL dP dS
rotmatvector (1:9)]]
>> *+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./OutBrick_run_022+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:./OutBrick_run_022+orig.BRIK is 4.199786 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./OutBrick_run_022+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:./OutBrick_run_022+orig.BRIK is 4.199786 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./OutBrick_run_022+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:./OutBrick_run_022+orig.BRIK is 4.199786 degrees from plumb.
3drefit -saveatr -atrint TAXIS_NUMS 350 72 77002 -999 -999 -999 -999 -999 OutBrick_run_022.slicemocoxy_afni.slomoco_pestica+orig
++ 3drefit: AFNI version=AFNI_16.2.17 (Sep 16 2016) [64-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset OutBrick_run_022.slicemocoxy_afni.slomoco_pestica+orig
++ 3drefit processed 0 datasets
3drefit -saveatr -atrfloat TAXIS_FLOATS 0 1.05 0 -31.762 2 -999999 -999999 -999999 OutBrick_run_022.slicemocoxy_afni.slomoco_pestica+orig
++ 3drefit: AFNI version=AFNI_16.2.17 (Sep 16 2016) [64-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset OutBrick_run_022.slicemocoxy_afni.slomoco_pestica+orig
++ 3drefit processed 0 datasets
3drefit -saveatr -atrfloat TAXIS_OFFSETS 0 0.44 0.8775 0.265 0.7025 0.0875 0.5275 0.9675 0.3525 0.79 0.175 0.615 0 0.44 0.8775 0.265 0.7025 0.0875 0.5275 0.9675 0.3525 0.79 0.175 0.615 0 0.44 0.8775 0.265 0.7025 0.0875 0.5275 0.9675 0.3525 0.79 0.175 0.615 0 0.44 0.8775 0.265 0.7025 0.0875 0.5275 0.9675 0.3525 0.79 0.175 0.615 0 0.44 0.8775 0.265 0.7025 0.0875 0.5275 0.9675 0.3525 0.79 0.175 0.615 0 0.44 0.8775 0.265 0.7025 0.0875 0.5275 0.9675 0.3525 0.79 0.175 0.615 OutBrick_run_022.slicemocoxy_afni.slomoco_pestica+orig
++ 3drefit: AFNI version=AFNI_16.2.17 (Sep 16 2016) [64-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset OutBrick_run_022.slicemocoxy_afni.slomoco_pestica+orig
++ 3drefit processed 0 datasets
3dNotes -h slicewise_moco_inplane.sh OutBrick_run_022+orig OutBrick_run_022.slicemocoxy_afni.slomoco_pestica+orig
Error: Cannot open dataset
===