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⇤ ← Revision 1 as of 2010-06-09 16:00:21
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| #before running script make sure you've typed: # freesurfer_4.0.1 # mne_setup_2.5 # setenv SUBJECTS_DIR /imaging/ef02/lexpro/subject # setenv SUBJECT 0319 |
## Your variables path='<myMEGdatapath>' # where your MEG fiff-files are MRIpath='/myMRIdirectory/' # where your MRI subdirectories are outpath='/myoutpath' # path for output files #condition names as used in file names to which inverse operator shall be applied conds=('cond1' 'cond2' 'cond3') |
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| ################ # PARAMETERS: |
# subjects names used for MRI data subjects=(\ 'Subject1' \ 'Subject1' \ 'Subject1' \ ) |
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| # Input/Output file path: | # MEG IDs (your directory structure may differ) subj_pre=(\ 'meg10_0001' \ 'meg10_0002' \ 'meg10_0003' \ ) |
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| #path='/megdata/cbu/PATH/TO/YOUR/DATA' path='/group/erp/data/caroline.coutout/MEG/data' MRIpath='/group/erp/data/caroline.coutout/MEG/MRIs' linkpath='/imaging/olaf/MEG/GoNoGo/STC' # necessary because of extra dot in "...olaf.hauk..." #condition names as used in file names conds=('lex_go' 'lex_nogo' 'lex_Go-NoGo' 'sem_go' 'sem_nogo' 'sem_Go-NoGo' 'freq_H' 'freq_L' 'freq_L-H') # number of effective averages for mne_make_movie --nave # not needed any more #naves=('100' '100' '100' '100' '120') |
# MEG subdirectories (your directory structure may differ) subj_dir=(\ '100001' \ '100002' \ '100003' \ ) |
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| subjects=(\ '2' \ '3' \ '4' \ '5' \ '6' \ '7' \ '8' \ # '9' \ # '10' \ # '11' \ # '12' \ # '13' \ # '14' \ # '15' \ # '16' \ # '17' \ # '18' \ # '19' \ # '20' \ # '21' \ # '22' \ ) |
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| subj_pre=(\ 'meg10_0047' \ 'meg10_0083' \ 'meg10_0084' \ 'meg10_0085' \ 'meg10_0086' \ 'meg10_0087' \ 'meg10_0088' \ # 'meg10_0091' \ # 'meg10_0094' \ # 'meg10_0096' \ # 'meg10_0098' \ # 'meg10_0101' \ # 'meg10_0101' \ # 'meg10_0102' \ # 'meg10_0104' \ # 'meg10_0106' \ # 'meg10_0108' \ # 'meg10_0109' \ # 'meg10_0110' \ # 'meg10_0112' \ # 'meg10_0114' \ ) subj_dir=(\ '100317' \ '100407' \ '100408' \ '100409' \ '100409' \ '100412' \ '100412' \ # '100413' \ # '100414' \ # '100415' \ # '100415' \ # '100416' \ # '100416' \ # '100419' \ # '100419' \ # '100420' \ # '100420' \ # '100421' \ # '100422' \ # '100422' \ # '100423' \ ) |
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| # REPORT number of files to be processed: |
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| echo " " | |
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| echo " " echo " " |
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| --subject Subject${subjects[m]} \ --inv ${path}/${subj_pre[m]}/${subj_dir[m]}/${subj_pre[m]}_1L-fixed-inv.fif \ |
--subject {subjects[m]} \ --inv --inv ${path}/${subj_pre[m]}_0${subjects[m]}/${subj_dir[m]}/YourName_1L-MEG-loose0.2-inv.fif \ |
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| --set 1 --morph average --smooth 5 \ --bmin -100 --bmax 0 \ --stc ${path}/STC/${subj_pre[m]}_${conds[c]} | tee -a GNG_make-movie.log |
--morph average \ --smooth 5 \ --bmin -100 \ --bmax 0 \ --stc ${outpath}/STC/${subj_pre[m]}_${conds[c]} done # conditions |
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| # symbolic links necessary because extra dot in "...olaf.hauk..." causes trouble! ln -s ${path}/STC/${subj_pre[m]}_${conds[c]}-lh.stc ${linkpath}/${subj_pre[m]}_${conds[c]}-lh.stc ln -s ${path}/STC/${subj_pre[m]}_${conds[c]}-rh.stc ${linkpath}/${subj_pre[m]}_${conds[c]}-rh.stc done # condition loop done # subject loop echo " " echo "DONE" echo " " # END OF SCRIPT ###################### |
done # subjects |
#
path='<myMEGdatapath>' # where your MEG fiff-files are MRIpath='/myMRIdirectory/' # where your MRI subdirectories are outpath='/myoutpath' # path for output files
#condition names as used in file names to which inverse operator shall be applied conds=('cond1' 'cond2' 'cond3')
# subjects names used for MRI data subjects=(\
- 'Subject1' \ 'Subject1' \ 'Subject1' \
)
# MEG IDs (your directory structure may differ) subj_pre=(\
- 'meg10_0001' \ 'meg10_0002' \ 'meg10_0003' \ )
# MEG subdirectories (your directory structure may differ) subj_dir=(\
- '100001' \ '100002' \ '100003' \
- )
# SCRIPT BEGINS HERE:
nsubjects=${#subjects[*]} lastsubj=expr $nsubjects - 1
nconds=${#conds[*]} lastcond=expr $nconds - 1
for m in seq 0 ${lastsubj} do
- echo " " echo " Computing movies for SUBJECT ${subjects[m]}" echo " "
for c in seq 0 ${lastcond} do
- # Current Estimates mne_make_movie \ --subject {subjects[m]} \
--inv --inv ${path}/${subj_pre[m]}_0${subjects[m]}/${subj_dir[m]}/YourName_1L-MEG-loose0.2-inv.fif \ --meas ${path}/${subj_pre[m]}/${subj_dir[m]}/${conds[c]}.fif \ --morph average \ --smooth 5 \ --bmin -100 \ --bmax 0 \ --stc ${outpath}/STC/${subj_pre[m]}_${conds[c]}
- # Current Estimates mne_make_movie \ --subject {subjects[m]} \
done # subjects