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The following script will produce the source space (downsampled version of the cortical surface in Freesurfer), which will be saved in a file ending in *-src.fif, which can be read into Matlab using mne_read_source_spaces. After this step, you should realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set). It is briefly described below. The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf MNE manual], [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers reading papers], and [http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagersInterestGroup discussions] with more experienced researchers. |
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| SUBJECTS_DIR='</myMRIdirectory/>' | SUBJECTS_DIR='</myMRIdirectory/>' # root directory for MRI data |
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| for SUBJECT in Subject1 Subject2Subject3 # use your subject names here | for SUBJECT in Subject1 Subject2 Subject3 # use your list of subject names here |
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| cd ${SUBJECTS_DIR} |
# creates surfaces necessary for BEM head models |
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rm $SUBJECTS_DIR/$SUBJECT/bem/inner_skull.surf rm $SUBJECTS_DIR/$SUBJECT/bem/outer_skull.surf rm $SUBJECTS_DIR/$SUBJECT/bem/outer_skin.surf rm $SUBJECTS_DIR/$SUBJECT/bem/brain_surface.surf |
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| # creates fiff-files for MNE describing MRI data | |
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| # create a source space from the cortical surface created in Freesurfer | |
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mri_convert -ot cor $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz $SUBJECTS_DIR/$SUBJECT/mri/T1/ mkheadsurf -subjid $SUBJECT |
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= Aligning MEG and MRI coordinate systems = This is a brief summary of how to align MEG and MRI coordinate systems. For more information see the MNE manual (chapter 12.11). Make sure you've typed mne_setup_2.6.0 setenv SUBJECTS_DIR </myMRIdirectory/> before proceeding. 1) Start mne_analyze. 2) Load a surface file (File -> Load Surface, choose inflated). 3) Load a fiff-file containing digitiser data (raw or averaged file; File -> Load digitizer data). 4) Open the view (View -> Show Viewer). 5) Click on Options. Hide the cortex, make the skin transparent, show the digitiser data. 6) Choose Adjust -> Coordinate Alignment. Define approximate landmarks (LAP, RAP, Nasion) by clicking at their labels, then at their approximate locations in the viewer. The click Align Using Fiducials. 7) The use the "ICP Align" option multiple times until the transformation matrix doesn't change significantly any more. You can remove outliers using the "Discard" option (e.g. choose 10 or 5 mm, then ICP align again). 8) When you are happy, click "Save MRI". |
Head Model and Source Space Creation in MNE
Make sure you've typed
mne_setup_2.6.0
freesurfer_4.3.0
setenv SUBJECTS_DIR </myMRIdirectory/>
in your Linux command window.
The following script will produce the source space (downsampled version of the cortical surface in Freesurfer), which will be saved in a file ending in *-src.fif, which can be read into Matlab using mne_read_source_spaces.
After this step, you should realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set). It is briefly described below.
The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf MNE manual], [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers reading papers], and [http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagersInterestGroup discussions] with more experienced researchers.
SUBJECTS_DIR='</myMRIdirectory/>' # root directory for MRI data
for SUBJECT in Subject1 Subject2 Subject3 # use your list of subject names here
do
# creates surfaces necessary for BEM head models
mne_watershed_bem --overwrite --subject $SUBJECT
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_inner_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/inner_skull.surf
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/outer_skull.surf
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skin_surface' $SUBJECTS_DIR/$SUBJECT/bem/outer_skin.surf
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_brain_surface' $SUBJECTS_DIR/$SUBJECT/bem/brain_surface.surf
# creates fiff-files for MNE describing MRI data
mne_setup_mri --overwrite --subject $SUBJECT
# create a source space from the cortical surface created in Freesurfer
mne_setup_source_space --spacing 5 --overwrite --subject $SUBJECT
done
Aligning MEG and MRI coordinate systems
This is a brief summary of how to align MEG and MRI coordinate systems. For more information see the MNE manual (chapter 12.11).
Make sure you've typed
- mne_setup_2.6.0
setenv SUBJECTS_DIR </myMRIdirectory/>
before proceeding.
1) Start mne_analyze.
2) Load a surface file (File -> Load Surface, choose inflated).
3) Load a fiff-file containing digitiser data (raw or averaged file; File -> Load digitizer data).
4) Open the view (View -> Show Viewer).
5) Click on Options. Hide the cortex, make the skin transparent, show the digitiser data.
6) Choose Adjust -> Coordinate Alignment. Define approximate landmarks (LAP, RAP, Nasion) by clicking at their labels, then at their approximate locations in the viewer. The click Align Using Fiducials.
7) The use the "ICP Align" option multiple times until the transformation matrix doesn't change significantly any more. You can remove outliers using the "Discard" option (e.g. choose 10 or 5 mm, then ICP align again).
8) When you are happy, click "Save MRI".