open-discussion > Secondorder motion correction errors
Apr 6, 2015  11:04 PM | Gabe Castillo
Secondorder motion correction errors
I'm having errors pop up about an hour into running slomoco on a dataset. This data was acquired obliquely in case that helps. Also, I have specified type 3 slice order(GE interleaved), but the 2nd order correction seems to go back to the default(1).

I should add that the setup_slomoco.sh script has the following line:
export PESTICA_SLICE_TIMING="siemens-alt-asc"
I don't know the correct text to specify GE ordered interleaved slicing.

It also seems that the matlab path is not being propagated correctly, as I have this line in setup_slomoco.sh:


export MATLAB_AFNI_DIR=/usr/local/afni_matlab


But when I use the path command in matlab, the BrikLoad command is successfully found

Any help would be appreciated. Please see output below:
Running Secondorder Motion Correction using SLOMOCO output

matlab <<<"addpath /usr/local/slomoco; mocoparams=read_motion_newslicealg('tempslmoco_volslc_alg_vol_213_PDF.PCOG14.WMEM1.slicemocoxy_afni/motion.wholevol_zt'); slicemoco_newalgorithm_input('213_PDF.PCOG14.WMEM1.slicemocoxy_afni+orig','213_PDF.PCOG14.WMEM1.brain+orig',mocoparams,3); exit;"

assuming slice timing==1, for interleaved ascending, siemens style
Wait, script starting...
Undefined function 'BrikLoad' for input arguments of type 'struct'.

Error in slicemoco_newalgorithm_input (line 17)
[err, im, ainfo, ErrMessage]=BrikLoad(ep2d_filename, Opt);

>> Undefined function 'BrikLoad' for input arguments of type 'struct'.

Error in qa_slomoco (line 14)
[err, ima, ainfo, ErrMessage]=BrikLoad(ep2d_filename, Opt);

>> *+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+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:213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+orig.BRIK is 14.743005 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+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:213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+orig.BRIK is 14.743005 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+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:213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+orig.BRIK is 14.743005 degrees from plumb.
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Feb 9 2015) [64-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset 213_PDF.PCOG14.WMEM1.slicemocoxy_afni.zalg_moco2+orig
++ 3drefit processed 0 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Feb 9 2015) [64-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset 213_PDF.PCOG14.WMEM1.slicemocoxy_afni.zalg_moco2+orig
++ 3drefit processed 0 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Feb 9 2015) [64-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset 213_PDF.PCOG14.WMEM1.slicemocoxy_afni.zalg_moco2+orig
++ 3drefit processed 0 datasets

Error: Cannot open dataset

EDIT: Added some relevant info regarding startup script and matlab path variables.
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TitleAuthorDate
Secondorder motion correction errors
 Gabe Castillo Apr 6, 2015
Gabe Castillo Apr 7, 2015
Erik Beall Apr 9, 2015
Gabe Castillo Apr 11, 2015
Gabe Castillo Apr 7, 2015