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| Deletions are marked like this. | Additions are marked like this. |
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| '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_preprocessing Pre-processing MRI Data in Freesurfer]:''' | |
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| '''Segment Head Surfaces:''' mne_watershed_bem |
* mri_convert * recon-all '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Segment Head Surfaces]:''' |
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| '''Prepare MRI Data for MNE:''' mne_setup_mri |
* mne_watershed_bem '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Prepare MRI Data for MNE]:''' |
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| '''Prepare Source Space (Cortical Surface) for MNE:''' mne_setup_source_space |
* mne_setup_mri '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Prepare Source Space (Cortical Surface) for MNE]:''' |
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| '''Align MEG and MRI coordinate systems''' mne_analyze |
* mne_setup_source_space '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Align MEG and MRI coordinate systems]:''' |
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| '''Set Up BEM Information for MNE:''' mne_setup_forward_model |
* mne_analyze '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution Set Up BEM Information for MNE]:''' |
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| '''Compute Forward Solution:''' mne_do_forward_solution |
* mne_setup_forward_model '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution Compute Forward Solution]:''' |
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| '''Average MEG Data, Compute Covariance Matrix:''' mne_process_raw |
* mne_do_forward_solution '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Averaging Average MEG Data], [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_CovarianceMatrix Compute Covariance Matrix]:''' |
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| '''Compute Average Cortical Surface:''' make_average_subject |
* mne_process_raw '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Compute Average Cortical Surface]:''' |
| Line 27: | Line 29: |
| '''Create Inverse Operator (from Forward Solution):''' mne_do_inverse_operator |
* make_average_subject '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator Create Inverse Operator (from Forward Solution)]:''' |
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| '''Compute Source Estimates (Apply Inverse Operator to MEG data):''' mne_make_movie |
* mne_do_inverse_operator '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Compute Source Estimates (Apply Inverse Operator to MEG data)]:''' |
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| '''Average Source Estimates:''' mne_average_estimates |
* mne_make_movie '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Average Source Estimates]:''' |
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| '''Extract ROI data:''' mne_make_movie |
* mne_average_estimates '''[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels Extract ROI data]:''' |
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| '''Visualisation:''' mne_analyze |
* mne_make_movie |
Overview of MNE Processing Steps and Commands
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_preprocessing Pre-processing MRI Data in Freesurfer]:
- mri_convert
- recon-all
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Segment Head Surfaces]:
- mne_watershed_bem
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Prepare MRI Data for MNE]:
- mne_setup_mri
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Prepare Source Space (Cortical Surface) for MNE]:
- mne_setup_source_space
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing Align MEG and MRI coordinate systems]:
- mne_analyze
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution Set Up BEM Information for MNE]:
- mne_setup_forward_model
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution Compute Forward Solution]:
- mne_do_forward_solution
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Averaging Average MEG Data], [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_CovarianceMatrix Compute Covariance Matrix]:
- mne_process_raw
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Compute Average Cortical Surface]:
- make_average_subject
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator Create Inverse Operator (from Forward Solution)]:
- mne_do_inverse_operator
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Compute Source Estimates (Apply Inverse Operator to MEG data)]:
- mne_make_movie
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates Average Source Estimates]:
- mne_average_estimates
[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels Extract ROI data]:
- mne_make_movie