open-discussion
open-discussion > sharing a solution to fixing errors running slomoco
Apr 12, 2018 05:04 PM | Yuqi Liu - University of Delaware
sharing a solution to fixing errors running slomoco
I recently started using pestica4 and kept getting errors running
slicemoco_newalgorithm.sh. After some inspections I fixed it, and
want to share with other uses.
So after typing slicemoco_newalgorithm.sh -d , I got errors below during secondorder motor correction:
----------------------------------------------------
----------------------------------------------------
finished slicewise in-plane motion correction
Exiting
Running Secondorder Motion Correction using SLOMOCO output
matlab -nodesktop -nosplash addpath /Users/yuqiliu/Downloads/pestica4/slomoco; addpath /Users/yuqiliu/Downloads/pestica4/afni_matlab; addpath /Users/yuqiliu/Downloads/pestica4/pestica_matlab; slicemoco_newalgorithm_input('tactile_run1.slicemocoxy_afni+orig','tactile_run1.brain+orig','tempslmoco_volslc_alg_vol_tactile_run1.slicemocoxy_afni/motion.wholevol_zt'); exit;
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016b (9.1.0.441655) 64-bit (maci64)
September 7, 2016
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).
Output argument "tranmat_zt" (and maybe others) not assigned during call to
"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
-----------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------
I went back to functions involved in the error message and figured it the problem was due to the command gawk not found. Installing gawk solved my problem.
Best,
Yuqi
So after typing slicemoco_newalgorithm.sh -d , I got errors below during secondorder motor correction:
----------------------------------------------------
----------------------------------------------------
finished slicewise in-plane motion correction
Exiting
Running Secondorder Motion Correction using SLOMOCO output
matlab -nodesktop -nosplash addpath /Users/yuqiliu/Downloads/pestica4/slomoco; addpath /Users/yuqiliu/Downloads/pestica4/afni_matlab; addpath /Users/yuqiliu/Downloads/pestica4/pestica_matlab; slicemoco_newalgorithm_input('tactile_run1.slicemocoxy_afni+orig','tactile_run1.brain+orig','tempslmoco_volslc_alg_vol_tactile_run1.slicemocoxy_afni/motion.wholevol_zt'); exit;
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016b (9.1.0.441655) 64-bit (maci64)
September 7, 2016
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).
Output argument "tranmat_zt" (and maybe others) not assigned during call to
"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
-----------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------
I went back to functions involved in the error message and figured it the problem was due to the command gawk not found. Installing gawk solved my problem.
Best,
Yuqi