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⇤ ← Revision 1 as of 2010-06-10 11:44:55
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| #before running script make sure you've typed: # freesurfer_4.0.1 # mne_setup_2.6 # setenv SUBJECTS_DIR /imaging/ef02/lexpro/subject # setenv SUBJECT 0319 |
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| ## Your variables | |
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| ################ # PARAMETERS: # Input/Output file path: #path='/megdata/cbu/PATH/TO/YOUR/DATA' path='/group/erp/data/olaf.hauk/MEG/GoldStandard/data' |
datapath='<myMEGdatapath>' # where your MEG fiff-files are |
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| subjects=(\ '091015' \ '100217' \ '090615' \ '100309' \ '100310' \ ) |
# MEG IDs (your directory structure may differ) subj_pre=(\ 'meg10_0001' \ 'meg10_0002' \ 'meg10_0003' \ ) |
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| # MEG subdirectories (your directory structure may differ) | |
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| 'meg09_0306' \ 'meg10_0010' \ 'meg09_0171' \ 'meg10_0030' \ 'meg10_0032' \ ) |
'100001' \ '100002' \ '100003' \ ) |
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| ##################### # SCRIPT BEGINS HERE: |
## Processing: |
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| echo " " | |
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| echo " " echo " " |
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| --raw ${inpath}/block1_raw_mf.fif \ --raw ${inpath}/block2_raw_mf.fif \ --raw ${inpath}/block3_raw_mf.fif \ --raw ${inpath}/block4_raw_mf.fif \ --eventsout ${inpath}/block1_raw_mf_events.txt \ --eventsout ${inpath}/block2_raw_mf_events.txt \ --eventsout ${inpath}/block3_raw_mf_events.txt \ --eventsout ${inpath}/block4_raw_mf_events.txt \ --ave GSTD_mne_average_SpecFile.ave \ --gave ${inpath}/gave.fif \ |
--raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1.fif \ --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2.fif \ --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3.fif \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1-eve.txt \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2-eve.txt \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3-eve.txt \ --ave YourSpecificationFile.ave \ --gave ${datapath}/${subj_dir[m]}/${subjects[m]}/gave.fif \ |
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| --highpass 0.2 \ | --highpass 0.1 \ |
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| mne_process_raw \ --raw ${inpath}/block1_raw_mf.fif \ --raw ${inpath}/block2_raw_mf.fif \ --raw ${inpath}/block3_raw_mf.fif \ --raw ${inpath}/block4_raw_mf.fif \ --events ${inpath}/block1_raw_mf_events_cov.txt \ --events ${inpath}/block2_raw_mf_events_cov.txt \ --events ${inpath}/block3_raw_mf_events_cov.txt \ --events ${inpath}/block4_raw_mf_events_cov.txt \ --projoff \ --cov GSTD_mne_cov_SpecFile.cov \ --savecovtag cov \ --gcov ${inpath}/gcov.fif \ --highpass 0.2 #--cov MM.cov --savecovtag -cov done # subject loop echo " " echo "DONE" echo " " # END OF SCRIPT ###################### |
done # subjects |
#
datapath='<myMEGdatapath>' # where your MEG fiff-files are
# path to event files eventpath='/group/erp/data/olaf.hauk/Others/Miozzo/Stimuli/Event_Files/MNE'
# MEG IDs (your directory structure may differ) subj_pre=(\
- 'meg10_0001' \ 'meg10_0002' \ 'meg10_0003' \ )
# MEG subdirectories (your directory structure may differ) subj_dir=(\
- '100001' \ '100002' \ '100003' \
- )
nsubjects=${#subjects[*]} lastsubj=expr $nsubjects - 1
# REPORT number of files to be processed:
for m in seq 0 ${lastsubj} do
- echo " " echo " Averaging SUBJECT ${subjects[m]}" echo " " inpath=${path}'/'${subj_dir[m]}'/'${subjects[m]} echo ${inpath} mne_process_raw \
- --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1.fif \ --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2.fif \ --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3.fif \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1-eve.txt \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2-eve.txt \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3-eve.txt \
--ave YourSpecificationFile.ave \ --gave ${datapath}/${subj_dir[m]}/${subjects[m]}/gave.fif \ --saveavetag _avg \ --highpass 0.1 \ --projoff
- --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1.fif \ --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2.fif \ --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3.fif \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1-eve.txt \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2-eve.txt \ --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3-eve.txt \
done # subjects