Dear mne users,
at first and before all: Happy New Year to the list!
Then, back to work 
:
I recently tried to compute separate forward models for MEG, EEG and
combined EEG/MEG with the mne suite and mne_do_forward_solution
here is the bash code I used for the MEG-only computations:
arr1=($ListSubj)
Dir=/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/
for i in {0..19}; do
echo ${arr1[i]}export SUBJECTS_DIR=/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/mri/
export SUBJECT=\{arr1\[i\]\} export MEG\_DIR=/neurospin/meg/meg\_tmp/MTT\_MEG\_Baptiste/MEG/{arr1[i]}/mne_python# for MEG
mne_setup_source_space --ico 5 -overwrite
mne_setup_forward_model --homog --surf --ico 4mne_do_forward_solution --mindist 5 --spacing ico-5 --mricoord
Dir{arr1[i]}/raw_sss/run3_DG_trans_sss-trans.fif --meas
Dir{arr1[i]}/raw_sss/run3_DG_trans_sss.fif --bem ${arr1[i]}-5120.fif
--megonly --overwrite --fwd $MEG_DIR/run3_ico-5_megonly_-fwd.fifdone
and it worked fine.
For EEG only, I modified the code to use a 3 layer BEM (remove --homog
option in mne_setup_forward_model) and use the --eegonly option in
mne-do-forward solution.
arr1=($ListSubj)
Dir=/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/
for i in {0..1}; do
echo ${arr1[i]}export SUBJECTS_DIR=/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/mri/
export SUBJECT=\{arr1\[i\]\} export MEG\_DIR=/neurospin/meg/meg\_tmp/MTT\_MEG\_Baptiste/MEG/{arr1[i]}/mne_python# for EEG
mne_setup_source_space --ico 5 -overwrite
mne_setup_forward_model --surf --ico 4mne_do_forward_solution --mindist 5 --spacing ico-5 --mricoord
Dir{arr1[i]}/raw_sss/run3_DG_trans_sss-trans.fif --meas
Dir{arr1[i]}/raw_sss/run3_DG_trans_sss.fif --bem ${arr1[i]}-5120.fif
--eegonly --overwrite --fwd $MEG_DIR/run3_ico-5_eegonly_-fwd.fifdone
Then I got this error:
Read 306 MEG channels from
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/cb130477/raw_sss/run3_DG_trans_sss.fif
Read 61 EEG channels from
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/cb130477/raw_sss/run3_DG_trans_sss.fif
MEG not requested. MEG channels omitted.
Some EEG channels do not have locations assigned.
Forward computation failed (see above)
As I understood, if EEG channel number >60, it could raise an error and
prevent mne to retrieve channel location.
So I tried the dedicated fix: mne_check_eeg_locations
mne_check_eeg_locations --file
Dir{arr1[i]}/raw_sss/run3_DG_trans_sss-trans.fif --fix
and got:
mne_check_eeg_locations version 1.2 compiled at Jan 5 2015 04:22:49
input file :
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/sd130343/raw_sss/run3_DG_trans_sss-trans.fif
digitizer data file :
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/wl130316/raw_sss/run3_DG.fifChecking...
Could not find the channel information.
I suspect that the EEG064 reference is the problem so I try to modify
directly the EEG status of this channel with mne_rename_channels and the
following alias: "EEG064:MISC666:502" in a text file, trying to transform
this problematic channel into a harmless MISC.
mne_rename_channels --fif
Dir{arr1[i]}/raw_sss/run3_DG_trans_sss-trans.fif --alias
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/SCRIPTS/define_aliases.txt
and got:
mne_rename_channels version 1.5 compiled at Jan 5 2015 04:17:51
fif file :
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/sd130343/raw_sss/run3_DG_trans_sss-trans.fif
alias file :
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/SCRIPTS/define_aliases.txt
1 aliases read from
/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/SCRIPTS/define_aliases.txt
0 changes done
So it appears that it didn't change anything.
I checked that this EEG064 is in the fiff file and I confirmed it exists
from fiedtrip header content of the same file.
I'm a bit stuck at this step and would appreciate any feedback on my
unlucky attempts :).
Best regards,
Baptiste