open-discussion
open-discussion > RE: Secondorder motion correction errors
Apr 7, 2015 12:04 AM | Gabe Castillo
RE: Secondorder motion correction errors
I fixed the afni_matlab path issue, but the script continues to
assume slice timing to be 1 or siemens-alt-asc. I have tried
setting the value of PESTICA_SLICE_TIMING to 3(no quotes) and "3"
(with-quotes) in the setup script(and running it prior to slomoco)
to no avail.
> setup_slomoco.sh
setting up for PESTICA+SLOMOCO environment because it is not already setup
> slicemoco_newalgorithm.sh -d 213_PDF.PCOG14.WMEM1 -s 3
setting SLCMOCO_DIR to directory where this script is located (not the CWD)
***** Using copied input in 213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+orig.HEAD as input timeseries
***** Using 213_PDF.PCOG14.WMEM1.brain+orig.HEAD to mask out non-brain voxels
> setup_slomoco.sh
setting up for PESTICA+SLOMOCO environment because it is not already setup
> slicemoco_newalgorithm.sh -d 213_PDF.PCOG14.WMEM1 -s 3
setting SLCMOCO_DIR to directory where this script is located (not the CWD)
***** Using copied input in 213_PDF.PCOG14.WMEM1_pestica/213_PDF.PCOG14.WMEM1+orig.HEAD as input timeseries
***** Using 213_PDF.PCOG14.WMEM1.brain+orig.HEAD to mask out non-brain voxels
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;"
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>>
tdim =
tdim =
240
zdim =
37
assuming slice timing==1, for interleaved
ascending, siemens style
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Threaded View
| Title | Author | Date |
|---|---|---|
| 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 | |