Differences between revisions 9 and 58 (spanning 49 versions)

DBA tutorial: Compute sources in deep cerebral structures

Authors: Jean-Eudes Le Douget, Francois Tadel, Denis Schwartz

This tutorial explains step-by-step how to use the DBA (Deep Brain Activity) functionality, useful to assess subcortical source localization.

Contents

Import database
Select deep structures
Source estimation
Compute statistics
Volume scouts
DBA constraints [TODO]
References

Import database

This tutorial is based on resting-state recordings for 7 subjects with two conditions: eyes open (YO), eyes closed (YF). We have recorded 20 runs of 15 seconds for each subject and each condition.

The goal is to compute the contrast between the two conditions in the alpha band. The data has already been filtered in the alpha frequency band (7-13Hz) and the default anatomy is used for all the subjects.

Start by downloading the tutorial dataset TutorialDba.zip from the Download page.
The file is an exported Brainstorm protocol. To load it in your database, use the menu:
File > Load Protocol > Load from zip file.

Select deep structures

The first step consists in creating the surface file that includes the cortex and the deep structures that we want to include in the model. Here, in the default anatomy:

Right-click on "aseg atlas" > Less vertices > 15000 vertices.
Double-click on "aseg atlas_15000V" (contains the subcortical structures from the FreeSurfer altas).
Select the amygdala, the thalamus and the hippocampus, and create a subatlas.
Merge the cortex with the selected structures. Rename the new surface in "cortex_mixed".
Open the cortex_mixed surface and create a new atlas "Source model options". With Matlab 2015b+, the display looks weird because it limits the number of possible transparent layers to 5. To produce nicer figures, disable the OpenGL renderer (File > Edit preferences). The display will be much slower, but the renderer won't suffer from this limitation.
Set the set modeling options to "Deep brain" for all the structures.

Source estimation

Head model

In Process1, select all the subject folders. Click on [Process recordings].
Run process Sources > Compute head model: Custom source model, MEG=Overlappling spheres.
You can explore the source grids that were computed. Right-click on one of the head models > Check source grid (volume) and Check source grid (surface).

Inverse model

The noise covariance matrix was estimated from the empty room recordings (Empty_Subject) and copied to all the folders of all the subjects.

At this stage, it is now possible to compute sources.

You can now visualize activity the same way as for usual headmodels.

If activities of the volume structures (thalamus and amygdala here) do not appear, try moving the Min size cursor to max and then back to 1.

Compute statistics

Now that the source calculations are done, we design a statistical analysis to assess the eyes-open and eyes-closed contrast.

First, the alpha-power is time-averaged for each run
Then, the "Process2" tab is used : place the source power files of the eyes-closed condition in the "Files A" space and of the eyes-open condition in the "Files B" space.
To gain time, it is possible to sort the functional data by conditions, place the subjects in "FilesA" and "FilesB" and use the filter to include only files that contain 'avg' (for time-averaged files)
Run a Student's T-Test to compute a statistical contrast between the conditions
The stat file can then be visualized and the values corresponding to subcortical structures are also appearing
It is also interesting to observe the difference of means between conditions. To compute this, instead of runnning a Student's T-Test, select the "Difference of means" option

Volume scouts

Some subcortical structures are modeled as volume source structures (for instance here, the thalamus and the amygdala). It is not possible to display scouts time series for these structures from the "Source model" or "Structures" atlases. It is necessary to create a new atlas, specific to volume scouts. The steps are the following :

First, create the volume atlas
Second, to create a new scout :
- Click on the "Create scout" cross, and click one point of the structure you want to include in the scout
- Click on the "Increase scout size" as many times as necessary to include all the points of the volume, for example in the right thalamus
- Rename the scout and set the correct region and the desired function
- Repeat this operation for all the volume scouts you want to create
Finally, you can display time series of your choice

DBA constraints [TODO]

Describe the constraints applied to each region.

References

Attal Y, Bhattacharjee M, Yelnik J, Cottereau B, Lefèvre J, Okada Y, Bardinet E, Chupin M, Baillet S (2009)
Modelling and detecting deep brain activity with MEG and EEG
IRBM, 30(3):133-138

Attal Y, Schwartz D (2013)
Assessment of Subcortical Source Localization Using Deep Brain Activity Imaging Model with Minimum Norm Operators: A MEG Study
PLOS ONE, 8(3):e59856

Dumas T, Dubal S, Attal Y, Chupin M, Jouvent R (2013)
MEG Evidence for Dynamic Amygdala Modulations by Gaze and Facial Emotions
PLOS ONE, 8(9): e74145

-  ⇤ ← Revision 9 as of 2015-07-07 15:01:49 → 
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+   ← Revision 58 as of 2016-08-10 13:16:14 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
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-= Compute sources in deep cerebral structures : DBA tutorial =
+= DBA tutorial: Compute sources in deep cerebral structures =
''Authors: Jean-Eudes Le Douget, Francois Tadel, Denis Schwartz''
-Line 4:
+Line 6:
-== Import Database ==
To follow through the tutorial, the dataset can be downloaded *here*.
+<<TableOfContents(2,2)>>
-Line 7:
+Line 8:
-It contains MEG resting-state recordings of 7 subjects under 2 conditions, eyes-open (YO) and eyes-closed (YF). For each subject and under each condition, 20 runs of 15 seconds are included in the dataset.
+== Import database ==
This tutorial is based on resting-state recordings for 7 subjects with two conditions: eyes open (YO), eyes closed (YF). We have recorded 20 runs of 15 seconds for each subject and each condition.
-Line 9:
+Line 11:
-The dataset is already in Brainstorm format and simply needs to be loaded  via File > Load Protocol. [[attachment:LoadProtocol]]
+The goal is to compute the contrast between the two conditions in the alpha band. The data has already been filtered in the alpha frequency  band (7-13Hz) and the default anatomy is used for all the  subjects.
-Line 11:
+Line 13:
-The following steps detail a method to compute the Eyes-Open vs Eyes-Closed contrast in the alpha band.

Note that the runs have already been filtered in the alpha frequency band (7-13Hz) and that for simplicity, default anatomy is used for all subjects.
+ * Start by downloading the tutorial dataset '''TutorialDba.zip''' from the [[http://neuroimage.usc.edu/bst/download.php|Download]] page.
 * The file is an exported Brainstorm protocol. To load it in your database, use the menu:<<BR>> File > Load Protocol > '''Load from zip file'''. <<BR>><<BR>> {{attachment:loadzip.gif}}
-Line 16:
+Line 17:
-The first step consists in creating the surface file that includes the cortex and the deep structures that wa want to include in the model.
Here, in the default anatomy:
+The first step consists in creating the surface file that includes the cortex and the deep structures that we want to include in the model. Here, in the default anatomy:
 Line 19:
- * Double-click on "aseg atlas" (which contains the subcortical structures)
 * Select the amygdala, the thalamus and the hippocampus, and create a subatlas
+ * Right-click on "aseg atlas" > '''Less vertices''' > '''15000''' vertices. <<BR>><<BR>> {{attachment:aseg_downsample.gif||height="213",width="436"}}
 * Double-click on "aseg atlas_15000V" (contains the subcortical structures from the FreeSurfer altas).

 * Select the amygdala, the thalamus and the hippocampus, and create a subatlas. <<BR>><<BR>> {{attachment:aseg_keep.gif||height="385",width="555"}}

 * '''Merge '''the cortex with the selected structures. '''Rename '''the new surface in "cortex_mixed". <<BR>><<BR>> {{attachment:aseg_merge.gif}}  {{attachment:aseg_rename.gif}}

 * Open the cortex_mixed surface and create a new atlas "'''Source model options'''". With Matlab 2015b+, the display looks weird because it limits the number of possible transparent layers to 5. To produce nicer figures, disable the OpenGL renderer (File > Edit preferences). The display will be much slower, but the renderer won't suffer from this limitation.<<BR>><<BR>> {{attachment:atlas_model.gif||height="214",width="668"}}

 * Set the set modeling options to "'''Deep brain'''" for all the structures.<<BR>><<BR>> {{attachment:atlas_dba.gif||height="246",width="606"}}

== Source estimation ==
==== Head model ====
 * In Process1, select all the subject folders. Click on [Process recordings].
 * Run process '''Sources > Compute head model''': Custom source model, MEG=Overlappling spheres. <<BR>><<BR>> {{attachment:dba_headmodel.gif}}
 * You can explore the source grids that were computed. Right-click on one of the head models > '''Check source grid (volume)''' and '''Check source grid (surface)'''. <<BR>><<BR>>{{attachment:headmodel_grid.gif}}

==== Inverse model ====
 * The noise covariance matrix was estimated from the empty room recordings (Empty_Subject) and copied to all the folders of all the subjects.
-Line 23:
+Line 40:
-== Compute Noise Covariance matrix ==
== Compute source activity ==
== Visualize activity ==
+At this stage, it is now possible to compute sources.

{{attachment:DBA_ComputeSources.png||height="244",width="171"}}    {{attachment:DBA_SourceOptions.png||height="232",width="156"}}       {{attachment:DBA_SourceOptions2.png||height="289",width="143"}}

You can now visualize activity the same way as for usual headmodels.

{{attachment:DBA_VisuActivity.png||height="351",width="478"}}

If activities of the volume structures (thalamus and amygdala here) do not appear, try moving the Min size cursor to max and then back to 1.
-Line 27:
+Line 51:
+Now that the source calculations are done, we design a statistical analysis to assess the eyes-open and eyes-closed contrast.

 * First, the alpha-power is time-averaged for each run<<BR>><<BR>> {{attachment:DBA_AverageTime.png||height="259",width="303"}}       {{attachment:DBA_AverageTimeOptions.png||height="216",width="236"}}

 * Then, the "Process2" tab is used : place the source power files of the eyes-closed condition in the "Files A" space and of the eyes-open condition in the "Files B" space.<<BR>>To gain time, it is possible to sort the functional data by conditions, place the subjects in "FilesA" and "FilesB" and use the filter to include only files that contain 'avg' (for time-averaged files)
 * Run a Student's T-Test to compute a statistical contrast between the conditions<<BR>><<BR>> {{attachment:DBA_Ttest.png||height="422",width="383"}}     {{attachment:DBA_TtestOptions.png||height="283",width="226"}}
 * The stat file can then be visualized and the values corresponding to subcortical structures are also appearing<<BR>><<BR>> {{attachment:DBA_VisuStat.png||height="286",width="523"}}
 * It is also interesting to observe the difference of means between conditions. To compute this, instead of runnning a Student's T-Test, select the "Difference of means" option<<BR>><<BR>> {{attachment:DBA_DiffOfMeans.png||height="283",width="394"}}

== Volume scouts ==
Some subcortical structures are modeled as volume source structures (for instance here, the thalamus and the amygdala). It is not possible to display scouts time series for these structures from the "Source model" or "Structures" atlases. It is necessary to create a new atlas, specific to volume scouts. The steps are the following :

 * First, create the volume atlas<<BR>><<BR>> {{attachment:DBA_VolumeScouts.png||height="264",width="668"}}

 * Second, to create a new scout :
  * Click on the "Create scout" cross, and  click one point of the structure you want to include in the scout<<BR>>
 {{attachment:DBA_VolumeScout_FirstPoint.png||height="291",width="659"}}
  * Click on the "Increase scout size" as many times as necessary to include all the points of the volume, for example in the right thalamus<<BR>>
 {{attachment:DBA_IncreaseScoutSize2.png||height="239",width="148"}}                 {{attachment:DBA_Scout_RightThal.png||height="272",width="266"}}
  * Rename the scout and set the correct region and the desired function<<BR>><<BR>> {{attachment:DBA_RenameScout.png||height="78",width="192"}}
 {{attachment:DBA_SetRegion2.png||height="271",width="260"}}        {{attachment:DBA_SetFunction2.png||height="270",width="244"}}
  * Repeat this operation for all the volume scouts you want to create
 * Finally, you can display time series of your choice<<BR>><<BR>> {{attachment:DBA_DispolayScoutsTS.png||height="306",width="280"}}

== DBA constraints [TODO] ==
Describe the constraints applied to each region.

== References ==
Attal Y, Bhattacharjee M, Yelnik J, Cottereau B, Lefèvre J, Okada Y, Bardinet E, Chupin M, Baillet S (2009)<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/18003114|Modelling and detecting deep brain activity with MEG and EEG]]<<BR>>'''IRBM''', 30(3):133-138

Attal Y, Schwartz D (2013)<<BR>>[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059856|Assessment of Subcortical Source Localization Using Deep Brain Activity Imaging Model with Minimum Norm Operators: A MEG Study]]<<BR>>'''PLOS ONE''', 8(3):e59856

Dumas T, Dubal S, Attal Y, Chupin M, Jouvent R (2013)<<BR>>[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074145|MEG Evidence for Dynamic Amygdala Modulations by Gaze and Facial Emotions]]<<BR>>'''PLOS ONE''', 8(9): e74145

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