[Mne_analysis] computing forward solutions separately for MEG and EEG

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Wed Jan 7 12:13:52 EST 2015
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hi Baptiste,

it seems you did the right things in the right order.

are you sure the channel is called "EEG064" in the fif file? no space?
"EEG 064"?

otherwise to debug this please share the file or fire up a python
shell and inspect info obtained with

info = mne.io.read_info('fname_raw.fif')

HTH
Alex


On Wed, Jan 7, 2015 at 3:22 PM, Baptiste Gauthier
<gauthierb.ens at gmail.com> wrote:
> 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 4
>>
>> mne_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 $MEG_DIR/run3_ico-5_megonly_-fwd.fif
>>
>> done
>
>
> and it worked fine.
>
> For EEG only, I modified the code to use a 3 layer BEM (remove --homog
> option in mne_setup_forward_model) and use the --eegonly option in
> mne-do-forward solution.
>
>> arr1=($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 4
>>
>> mne_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.fif
>>
>> done
>
>
> 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.fif
>>
>> Checking...
>> 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
>
> --
> Baptiste Gauthier
> Postdoctoral Research Fellow
>
> INSERM-CEA Cognitive Neuroimaging unit
> CEA/SAC/DSV/DRM/Neurospin center
> Bât 145, Point Courier 156
> F-91191 Gif-sur-Yvette Cedex FRANCE
>
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