= SEEG Time-Frequency Fingerprint Analysis for Epileptogenic Zone Localization =
''Authors: Yash Shashank Vakilna, Chinmay Chinara, Johnson Hampson, Takfarinas Medani, Raymundo Cassani, John Mosher, Sylvain Baillet, Richard Leahy''

'''TODO: Add flowchart'''

It guides users through computing time-frequency decomposition maps to identify the epileptogenic zone (EZ) using both ictal and interictal SEEG data.

<<TableOfContents(3,2)>>

== Access the recordings ==
=== Link the recordings ===
 * Switch to the "functional data" view (2nd button, on top of the database explorer).
 * Right-click on the subject folder > '''Review raw file''':
  * Select the file format: '''EEG: EDF/EDF+'''
  * Select all the recordings: '''tutorial_seizure_fingerprinting/recordings/*.edf''' <<BR>><<BR>> {{attachment:15_import_link.png||width="650"}}
  * The selected recordings get added to the database.<<BR>><<BR>> {{attachment:15_import_link2.png||width="200"}}
 * The new files '''Link to raw file''' let you access directly the contents of the original SEEG files. The menu '''Review raw file''' does not actually copy any data to the database. [[http://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Review_vs_Import|More details]].

=== Import the contacts positions ===
In order to generate epileptogenicity maps, we need accurate 3D positions for the contacts of the depth electrodes. Placing the contacts requires a good understanding of the implantation scheme reported by the neurosurgeon, and some skills in reading MRI scans.

 * The channel file "EDF channels" contain the name of the channels, but not their positions. We need to import or edit separately the positions of the SEEG contacts.
 * Click on the '''[+]''' next to the four folders, select all the channel files simultaneously.
 * Right-click one channel file > '''Add EEG positions''' > '''From other studies''' > '''Implantation'''<<BR>><<BR>> {{attachment:83_import_pos_file_implantation.png||width="500"}}
 * At the end, you get a report indicating how many channels from the SEEG recordings were attributed a new 3D position. The channels are matched by name: the position file you import must include the labels of the channels and they must be named exactly in the the same way as in your recordings.<<BR>><<BR>> {{attachment:20_import_pos_report.png||width="500"}}
 * For '''EDF Channels''' under '''LVFA_and_wave''' and '''interictal_spike''', there were 12 channels not found. The type of the channels for which a position was not found is set to '''EEG_NO_LOC''', in order to ignore them when processing the SEEG data. In this example dataset, the channels numbered '''245 to 255''' and '''262''' are not found as they are not SEEG contacts.
 * For all the '''EDF Channels''', mark the channel '''MPS16''' as '''SEEG_NO_LOC''' because if not marked, when we [[https://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel|compute the forward head model]] using BEM surfaces it says that '''MPS16''' lies outside the BEM layer. Marking it excludes it from any future computations.
 * You should always validate that the type of all the channels has been detected correctly. Check also that the names are correct and using the same convention for all the contact of a given electrode. These are entered manually, and typing errors are frequent. Right-click on a channel file > '''Edit channel file'''.<<BR>><<BR>> {{attachment:16_edit_channel.png||width="650"}}
 * To edit one channel, double-click on the text to modify. To edit multiple channels, select them all and right-click > Set channel group/type. The column Group corresponds to the name of the depth electrode. It is detected based on the channel type and name. If you include as SEEG a channel that detected as something else or rename a channel, you would need to manually update the channel name.
 * If you don't have the positions for the SEEG contacts, or if they don't look correctly aligned, see the section [[https://neuroimage.usc.edu/brainstorm/Tutorials/SeizureFingerprinting#Edit_the_contacts_positions|Edit the contacts positions]] on how to tackle it.
 * To make this tutorial easier to reproduce and follow, we also distribute the positions of the contacts (that were localized as per the section above) [[https://neuroimage.usc.edu/brainstorm/Tutorials/SeizureFingerprinting#Export_the_contacts_position|exported as a .tsv file]] ('''tutorial_seizure_fingerprinting/recordings/Subject01_electrodes_mm.tsv'''). To import the contacts position from that refer to [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Import_the_contacts_positions|Epileptogenicity]] tutorial.

== Display the depth electrodes ==
=== 3D figures ===
 * Right-click on the channel file > '''Display sensors''' and explore all the available options.<<BR>><<BR>> {{attachment:23_display_menu.png||width="650"}}
 * You can render the SEEG depth electrodes in 3D together with the subject anatomy: surfaces, pre- or post-implantation volumes. You can add more anatomy elements to the figure with the button '''Add a surface''' ( {{attachment:iconSurfaceAdd.gif}} ) at the top-right of the '''Surface''' tab. For more help: [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#MRI_in_3D|Display the anatomy]].<<BR>><<BR>> {{attachment:24_display_3d.png||width="650"}}
 * Click on a contact to select it, right-click on it to get its name.<<BR>><<BR>> {{attachment:25_display_selectchan.png||width="500"}}

=== MRI Viewer ===
 * You can also display the contacts in the MRI viewer, on top of the the pre- or post-implantation volumes. By default, the electrode is displayed in a slice if there is a SEEG contact associated to it in the slice.<<BR>><<BR>> {{attachment:26_display_mri.png||width="600"}}
 * To display all the electrodes, select the option "'''MIP: Functional'''". For a glass-brain view, select at the same time the option "'''MIP: Anatomy'''".<<BR>><<BR>> {{attachment:27_display_mri_mip.png||width="600"}}
 * Zoom in/out with the buttons or the associated shortcuts (Ctrl+Scroll or +/-) and explore the volume with (Shift+)x/y/z. Additional display options are available in the popup menu for this figure. All the shortcuts are listed in [[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#Using_the_MRI_Viewer|this tutorial]].

=== Panel iEEG ===
 * When opening SEEG/ECOG recordings, the panel iEEG is added to the Brainstorm window. You can use it to edit the display properties of the depth electrodes. More details about the iEEG Panel can be found in the [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Panel_iEEG|Epileptogenicity]] tutorial. <<BR>><<BR>> {{attachment:29_panel_ieeg.png||width="650"}}

{{{#!wiki note
To know more about ways to display the SEEG recordings in Brainstorm refer to the [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Display_the_SEEG_recordings|Epileptogenicity]] tutorial.
}}}
== Review recordings ==
=== Power spectrum ===
We recommend that you start your data analysis with a power spectral density estimation of the recordings to check the quality of sensor recording. This is described in more details in the [[https://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter|Power spectrum]] tutorial.

 * In '''Process1''', select all the continuous files ('''Link to raw files''' or folders).<<BR>><<BR>> {{attachment:48_psd_process.png||width="650"}}
 * Double-click on the PSD files to display them. It can be seen that the power line interference at 60Hz along with its harmonics have been removed. This was done using a notch filter. More details can be found in the [[https://neuroimage.usc.edu/brainstorm/Tutorials/ArtifactsFilter#Apply_a_notch_filter|notch filter]] section in the above tutorial.<<BR>><<BR>> {{attachment:49_psd_result2.png||width="650"}}

=== Add events ===
We need to mark seizure onset event for the '''ictal''' and '''LVFA and wave''' recordings and spike event for '''interictal''' recording. There are events already available in recordings, that were marked for clinical use, to jump quickly to the page of interest. More details can be found in the tutorial [[https://neuroimage.usc.edu/brainstorm/Tutorials/EventMarkers|Event Markers]].

 * For '''LVFA and wave''', we will create a new event '''sEEG Onset''' at around 15s (center of the 30s recording extract).<<BR>><<BR>> {{attachment:51_mark_onset_law.png||width="650"}}
 * For '''ictal repetitive spike''', we will create a new event '''sEEG Onset''' at around 15s (center of the 30s recording extract).<<BR>><<BR>> {{attachment:50_mark_onset_irs.png||width="650"}}
 * For '''interictal spike''', we will create a new event '''Interictal spike''' at around 5s (center of the 10s recording extract).<<BR>><<BR>> {{attachment:52_mark_spike_is.png||width="650"}}

== Import epochs of interest ==
At this point of the analysis, we are still looking at the original files, no SEEG data was copied to the database. The montages are saved in the Brainstorm preferences, the new events are saved in the links of the database.

We are now going to import the three segment of recordings i.e. '''LVFA and wave''' , '''ictal repetitive spike''' and '''interictal spike''' which are a subset of the '''Baseline''' recording.

=== Import in database ===
 * Right click on '''LVFA_and_wave > Link to raw file > Import in database'''.
  * Time window: All (0 to 30.0495)
  * Split in time blocks: Disabled
  * Use events: Enabled, select '''sEEG Onset'''
  * Epoch time: '''[-15000, +15000] ms''' (imports -15s to 15s around the event '''sEEG Onset''')
  * Remove DC offset: Enabled. More details can be found [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epoching#Import_in_database|here]].
  * Resample: Disabled
  * Create a separate folder for each event type: Disabled
  * Click '''Import'''.<<BR>><<BR>> {{attachment:53_import_onset.png||width="650"}}
 * Repeat the same steps above for importing '''ictal repetitive spike''' into the database.
 * Repeat the same steps above for importing '''interictal spike''' into the database with the modification in the following options:
  * Time window: All (0 to 10.0495)
  * Use events: Enabled, select '''Interictal spike'''
  * Epoch time: '''[-5000, +5000] ms''' (imports -5s to 5s around the event '''Interictal spike''')
 * At the end, you should have three new folders '''LVFA and wave''' , '''ictal repetitive spike''' and '''interictal spike''', the same name as the original raw files, but without the tag '''RAW''' on top. These new folders contain copies of the SEEG recordings, if you delete these folders from the database explorer, you lose the recordings they contain.
 * The imported epochs are saved with a new timing: for '''LVFA and wave''' and '''ictal repetitive spike''', the reference time t=0s is now the event '''sEEG Onset''' and for '''Interictal spike''', the reference time t=0s is now the event '''Interictal spike''', which has been removed from the list. You can still see the other marker timings adjusted accordingly.<<BR>><<BR>> {{attachment:54_import_database.png||width="650"}}

=== Bipolar montage ===
We will run the rest of the analysis using a bipolar montage (bipolar-2). The montage selected in the Record tab is for visualization only, most processes ignore this selection and work only on the original common-referential montage. To compute bipolar montage on time series, we need to explicitly apply the montage to the recordings. More details can be found in tutorials [[https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor|Montage editor]] and [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#Bipolar_montage|Epileptogenicity]].

 * In '''Process1''', drag and drop all the imported recordings (either the folders or the files).
 * Run the process '''Standardize > Apply montage'''
  * Montage name: '''Subject01: SEEG (bipolar 2)[tmp]'''
  * Create new folders: '''Enabled'''<<BR>><<BR>> {{attachment:55_import_montage.png||width="650"}}
 * This process rewrites the channel files and data files in the selected folders. The position associated with a bipolar channel in the channel file is the middle of the segment between the two contacts (e.g. '''AH1-AH2''' is placed half-way between '''AH1''' and '''AH2'''). <<BR>><<BR>> {{attachment:56_import_montage_chan.png||width="650"}}

== Head modeling ==
The forward models depend on the subject's anatomy, including head size and geometry, tissue conductivity, the computational method, and sensor characteristics. In this section, we will use the Boundary Element Method (BEM) approach available in Brainstorm for constructing the head model for sEEG.

 * We will first generate the BEM head surfaces from the MRI. More details can be found in [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem#BEM_surfaces|OpenMEEG BEM]] tutorial. This will generate three surfaces '''head, outer skull and inner skull''' estimated from the '''head mask'''  and the '''cortex''' obtained from the segmentation. The BEM surfaces will be used for the BEM forward computation below.<<BR>><<BR>> {{attachment:57_head_modeling.png||width="600"}}

 * We will then compute the [[https://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel|forward head model]] using the [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem|OpenMEEG BEM]] method. Switch to functional tab, right-click on the '''interictal_spike > EDF channels > Compute head model'''.
  * Source space: '''Cortex surface'''
  * Forward modelling methods: '''SEEG: OpenMEEG BEM'''
  * Use only '''Brain''' in BEM layers and conductivities (corresponds to bem_innerskull surface) as other surfaces do not matter for SEEG.
  * Use default OpenMEEG options.<<BR>><<BR>> {{attachment:58_headmodeller_openmeeg.png||width="650"}}
 * A new head model will be added to the folder.<<BR>><<BR>> {{attachment:59_headmodeller_final.png||width="150"}}
 * Right click on the head model file > '''Copy to other folders'''. Since the other folders contain data collected from the same subject using the same set of electrodes, we do not need to recompute the head model for each of them separately.
 * '''View leadfield vectors''':
  * Right click on the head model file > '''View SEEG leadfield vectors'''
  * Select reference '''MC2''' and click '''OK'''
  * Click on the figure and press '''E''' to display the electrodes
  * Make sure scouts are unselected ('''Scout''' tab > '''ALL''' and '''SEL''' unselected)
  * '''Surface''' tab: transparency = '''90''' and press '''Shift+Up arrow''' till the arrows are visible. Press '''Up/down''' to change the Reference electrode, '''Right/Left''' to change the target. Close all figures once done.<<BR>><<BR>> {{attachment:60_leadfield_vector.png||width="650"}}

== Compute noise covariance matrix ==
 * We will compute the noise covariance matrix for the '''Baseline''' recording as per the tutorial [[https://neuroimage.usc.edu/brainstorm/Tutorials/NoiseCovariance|Noise covariance]].
 * Right click on the '''Baseline (RAW) > Link to raw file > Noise covariance > Compute from recordings '''. Keep the default values and click '''OK'''.<<BR>><<BR>> {{attachment:61_noise_covariance.png||width="650"}}
 * '''Noise covariance''' node gets added to the database.<<BR>><<BR>> {{attachment:61_noise_covariance2.png||width="400"}}
 * Right click on the '''Noise covariance''' and '''Copy to other folders'''.

== Modeling interictal spikes ==
=== Compute inverse model ===
 * We will compute the inverse model for the '''interictal_spike''' recording. For more details refer to the tutorials [[https://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation|Source estimation]] and [[https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource|Volume source estimation]].
 * Expand the '''interictal_spike''' folder, right click on '''OpenMEEG BEM > Compute sources [2018]'''.
  * Method: '''Minimum norm imaging'''
  * Measure: '''sLORETA'''
  * Source model: Dipole orientations: '''Constrained: Normal to cortex'''
  * Noise covariance regularization: '''Diagonal noise covariance'''
  * Regularization parameter: '''Signal-to-noise ratio: 3.00'''
  * Output mode: Inverse kernel only
  * Sensors: '''SEEG'''. Click '''OK'''. <<BR>><<BR>> {{attachment:62_inverse_model1.png||width="600"}}
 * Two files get added to database. To learn about '''inversion kernel''' and '''LINK''' files in database refer to [[https://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Computing_sources_for_single_trials|this section]].<<BR>><<BR>> {{attachment:62_inverse_model2.png||width="200"}}

=== Display sensor time series ===
 * '''Display time series'''
  * Right-click on recording '''Interictal spike > SEEG > Display time series'''
  * On the '''Record''' tab,  select montage '''SPS (bipolar 2)'''
  * Select the first peak of '''SPS10-SPS11 (Time 0.041s)'''.
 * '''Display 2D layout of the spike'''
  * Right-click on recording '''Interictal spike > SEEG > 2D Layout'''
  * Click '''[...]''' on the corner and set'''[-500, 500]''' as the time window. Doing this will enable visualizing 1s of data across all the sensors giving a more clear sense of where the different spikes are. <<BR>><<BR>> {{attachment:63_disp_ts_interictal.png||width="650"}}

=== View sources ===
 * '''Display on cortex'''
  * Right click on '''sLORETA (LINK) > Cortical activations > Display on cortex'''
  * Show sensors: '''Ctrl+L''' (electrodes)
  * Set colormap: '''Colorbar > Colormap:Sources > Permanent menu''', select '''Maximum: Global''', '''Contrast -0''', '''Brightness 0'''
  * Switch to '''Surface''' tab: '''Amplitude 26%''', '''Min size 13'''<<BR>><<BR>> {{attachment:64_view_inv_model_cortex.png||width="500"}}
 * '''Display on 3D MRI viewer'''
  * Right click on '''sLORETA (LINK) > Cortical activations > Display on MRI (3D)'''
  * Show sensors: '''Ctrl+L''' (electrodes)
  * Press '''M''' to go to voxel with maximum intensity<<BR>><<BR>> {{attachment:65_view_inv_model_mri3d.png||width="500"}}
 * '''Display on MRI viewer'''
  * Right click on '''sLORETA (LINK) > Cortical activations > Display on MRI (MRI Viewer)'''
  * Turn on '''MIP: Functional'''
  * Switch to '''Surface''' tab, Amplitude: 56%, and press '''M''' to select voxel with maximum intensity<<BR>><<BR>> {{attachment:66_view_inv_model_mri.png||width="500"}}

=== Atlases and scouts ===
 * Display sources on the cortical surface
  * Right click on '''sLORETA (LINK) > Cortical activations > Display on Cortex'''
  * In the '''Scout''' tab, use the drop box to select '''Desikan-Killiany''' and click on '''ALL'''. This atlas is provided by default in Brainstorm. '''Ctrl+L''' to show all electrodes.<<BR>><<BR>> {{attachment:67_atlas_dk.png||width="600"}}
 * Since all the electrodes in the data are implanted on the right hemisphere of the brain, it is better to edit this atlas to only have scouts defined for the right region and remove the rest. Also we can subdivide the atlas to smaller scout regions to have smaller ROIs that will help in having better and more focused time-frequency epileptogenic maps later in the tutorial.
  * In '''Scout''' tab, select all the scouts in the right hemisphere and then create a new atlas from the selected scouts by '''Atlas >'''''' New atlas > Copy selected scouts. '''It will create a new atlas named '''Desikan-Killiany_02'''. Rename it to '''Desikan-Killiany_RH''' where "RH" indicates right hemisphere.
  * '''Atlas > Subdivide atlas > Area > Area of the sub-regions: 5 '''(cm sq.). A total of 176 scouts will be created with smaller and more focused ROI.<<BR>><<BR>> {{attachment:68_atlas_dk_176.png||width="600"}}
 * To know more about scouts in Brainstorm refer to the tutorial [[https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts|Scouts]].

== Modeling ictal wave ==
Switch to the folder '''LVFA_and_wave''' (not the RAW folder) and repeat the steps to '''compute inverse model''' as per the section above and study the sensor time series and inverse modeling results.<<BR>><<BR>> {{attachment:69_disp_ts_wave.png||width="650"}} <<BR>><<BR>> {{attachment:70_view_inv_model_wave.png}}

== Modeling ictal onset with LVFA ==
=== Sensor space ===
==== Compute time-frequency decomposition ====
 * Navigate and expand '''LVFA_and_wave_bipolar_2''' folder
 * Delete any previous recordings in the '''Process 1''' tab below
 * Drag-and-drop recording file '''sEEG onset (#1) | bipolar 2''' in '''Process 1''', click '''[RUN]'''<<BR>><<BR>> {{attachment:71_time_freq_decomp_lvfa1.png||width="650"}}
 * Add the process: '''Frequency > Time-frequency (Morlet wavelets)'''
  * Sensor type: '''SEEG'''
  * Select '''Spectral flattening: Multiply output power values by frequency'''
  * Click '''Edit...'''
  * Frequency definition: '''Log (start:N:stop), 1:25:100'''
  * Central Frequency: '''1 Hz''', Time resolution (FWHM): '''6s'''. Click '''OK''' and '''Run'''.<<BR>><<BR>> {{attachment:71_time_freq_decomp_lvfa2.png||width="650"}}
 * A new node '''Power,1-100Hz (SEEG) | multiply''' gets added to the database.<<BR>><<BR>> {{attachment:71_time_freq_decomp_lvfa3.png||width="250"}}
 * For more details go through the tutorial [[https://neuroimage.usc.edu/brainstorm/Tutorials/TimeFrequency|Time-frequency]].

==== View time-frequency maps ====
 * Right click '''sEEG onset (#1) | bipolar 2 > Power,1-100Hz (SEEG) | multiply > All channels'''
 * Click on '''Log(Power)''' to bring out the essential features in the maps.
 * Click on '''Smooth display''' to apply a Gaussian kernel to the map so that the underlying pattern becomes clearer for viewing.
 * Click on '''SPS8-SPS9'''
 * Set colormap: right-click on '''Colorbar > Colormap: Timefreq > Permanent menu''', Turn-off '''[Absolute Value]'''(if on), '''Maximum: Local''', '''Contrast 49''' '''Brightness -65'''
 * Right-click on the colored time-frequency plot > '''Power Spectrum, Time Series'''<<BR>><<BR>> {{attachment:72_time_freq_map_lvfa.png||width="650"}}
 * The red marked area above is the high frequency activity. The bottom right area contains the pre-ictal spikes that is signature of seizure fingerprinting.

=== Source space ===
==== Extract scout time series ====
 * We are going to now extract a single time-series for each of these scouts that best defines it.
 * Switch to the folder '''LVFA_and_wave''' (not the RAW folder).
 * Drag-and-drop '''sLORETA: SEEG(Constr) 2018 (LINK)''' in '''Process 1''', click '''[RUN]'''<<BR>><<BR>> {{attachment:73_scout_time_series_lvfa1.png||width="450"}}
 * Add the process: '''Extract > Scout time series'''
  * Select '''Desikan-Killiany_RH'''.
  * Select scouts: Press '''Ctrl+A''' to select all the scouts in the box.
  * Select Scout function: '''PCA'''
 {{attachment:73_scout_time_series_lvfa2.png||width="350"}}
 * A new matrix file '''sEEG onset (#1) | 176 scouts''' gets added to the database.<<BR>><<BR>> {{attachment:73_scout_time_series_lvfa3.png||width="200"}}
 * Right click on matrix file '''sEEG onset (#1) | 176 scouts > Display as time series'''.<<BR>><<BR>> {{attachment:75_scout_time_series_lvfa2.png||width="450"}}

==== Compute time-frequency decomposition ====
 * Drag-and-drop matrix file '''sEEG onset (#1) | 176 scouts''' in '''Process 1''', click '''[RUN]'''
 * Rest of the steps are the same as the corresponding [[https://neuroimage.usc.edu/brainstorm/Tutorials/SeizureFingerprinting#Compute_time-frequency_decomposition|earlier section]] in sensor space.<<BR>><<BR>> {{attachment:74_time_freq_decomp_lvfa2.png||width="450"}}

==== View time-frequency maps ====
 * Right click on matrix file '''sEEG onset (#1) | 176 scouts > Power,1-100Hz | multiply > Time-freq: All matrices'''
 * Right click on matrix file '''sEEG onset (#1) | 176 scouts > Power,1-100Hz | multiply > Time-freq: One matrix'''. Set selected data as '''postcentral R.3'''.
 * Click on '''Log(Power)''', '''Smooth display'''.
 * Set colormap: right-click on '''Colorbar > Colormap: Timefreq > Permanent menu''', Turn-off '''[Absolute Value]'''(if on), '''Maximum: Local''', '''Contrast 52''' '''Brightness -63'''
 * Right-click on the colored time-frequency plot > '''Power Spectrum, Time Series'''<<BR>><<BR>> {{attachment:76_time_freq_map_lvfa2.png||width="650"}}
 * The red marked area above is the high frequency activity. The bottom right area contains the pre-ictal spikes that is signature of seizure fingerprinting. We can say that this patch of cortex '''postcentral R.3''' was most associated with the LVFA pattern.

== Modeling ictal onset with repetitive spiking ==
=== Sensor space ===
==== Display time-series ====
 * Expand the folder '''ictal_repetitive_spike_bipolar_2'''
 * Right click on '''sEEG onset (#1) | bipolar 2 > Display time series'''
 * Change Montage to '''PIN > PIN (orig)'''<<BR>><<BR>> {{attachment:77_time_series_ictal.png||width="650"}}

==== Compute time-frequency decomposition ====
Same as above sections. Only one change, set sensor type: '''PIN5-PIN6''' for '''Time-frequency (Morlet wavelets)''' process.<<BR>><<BR>> {{attachment:78_time_freq_decomp_ictal.png||width="650"}}

==== View time-frequency maps ====
 * Right click on file '''sEEG onset (#1) | bipolar 2 > Power,1-100Hz (PIN5-PIN6) | multiply > One channel'''.
 * Click on '''Log(Power)''', '''Smooth display'''.
 * Set colormap: right-click on '''Colorbar > Colormap: Timefreq > Permanent menu''', '''Maximum: local''', '''Contrast 23''' '''Brightness -60'''<<BR>><<BR>> {{attachment:79_time_freq_map_ictal.png||width="650"}}
 * The high frequency activity on the right is due to the rhythmic activity seen in the time series for PIN5-PIN6. On analyzing the time-frequency map, this activity is localized between 5Hz and 55Hz. So we need to filter this frequency range so that our results are more focused on the rhythmic activity.

=== Source space ===
==== Compute inverse model ====
 * Switch to the folder '''ictal_repetitive_spike'''
 * Repeat the steps as in the [[https://neuroimage.usc.edu/brainstorm/Tutorials/SeizureFingerprinting#Compute_inverse_model|previous section]].<<BR>><<BR>> {{attachment:80_inverse_model_ictal.png||width="250"}}

==== View sources ====
 * Right-click on '''sEEG onset (#1) > SEEG > Display time series'''.
 * Change Montage to '''PIN(orig)'''
 * Set frequency filter: High-pass: '''5Hz''', Low-pass: '''55Hz'''
 * '''Display sources on MRI viewer'''
  * Right-click on '''sLORETA: SEEG(Constr) 2018 (LINK) > Cortical activations > Display on MRI (MRI Viewer)'''
  * Set colormap: Right Click on '''Colorbar > Colormap: Sources > Permanent Menu''', '''Maximum: Custom [0, 2]'''
  * Click on '''Surface tab''', set '''Amplitude 33% '''<<BR>><<BR>> {{attachment:81_inverse_model_res_ictal.png||width="600"}}
 * The peak of the rhythmic activity localized on the patch of the cortex as seen in the MRI Viewer above.

== Additional Documentation ==
=== Forum discussions ===
 * [[https://neuroimage.usc.edu/forums/t/updating-seeg-coordinates/49097|Updating SEEG coordinates]]

==== Articles ====
 * Yash Shashank Vakilna, Deniz Atilgan, Johnson Hampson, Chinmay Chinara, Takfarinas Medani, Richard M. Leahy, Nuria Lacuey, Samden D. Lhatoo, Sandipan Pati, John C. Mosher, Jay R. Gavvala. <<BR>> [[https://doi.org/10.1002/acn3.70115|Time-Frequency Fingerprint Analysis in SEEG Source-Space to Identify the Epileptogenic Zone]]. <<BR>> Annals of Clinical and Translational Neurology 2025.

=== Related tutorials ===
 * [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity|Epileptogenicity]]
 * [[https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG|ECoG/sEEG tutorial]]

<<TAG(Advanced)>>

== Scripting ==
The following script from the Brainstorm distribution reproduces the analysis presented in this tutorial page: [[https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_seizure_fingerprinting.m|brainstorm3/toolbox/script/tutorial_seizure_fingerprinting.m]]

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