Integration with MRI and fMRI - Revision history

Jaehyun: /* Alignment of BESA and MRICoordinate Systems */

2021-12-17T13:46:44Z

‎Alignment of BESA and MRICoordinate Systems

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Jaehyun: /* Co-locating Dipoles and MRI Locations */

2021-12-17T13:40:55Z

‎Co-locating Dipoles and MRI Locations

Dominik at 13:14, 25 November 2021

2021-11-25T13:14:21Z

Dominik at 13:10, 25 November 2021

2021-11-25T13:10:20Z

Robert: /* Introduction */

2021-05-06T07:06:02Z

‎Introduction

Robert: /* Define a Dipole in BESA Research at a Location Defined in the MRI */

2021-05-06T07:05:04Z

‎Define a Dipole in BESA Research at a Location Defined in the MRI

Robert: /* How to Generate a Brain Surface Mesh */

2021-05-06T07:03:44Z

‎How to Generate a Brain Surface Mesh

Robert: /* Alignment of BESA and MRICoordinate Systems */

2021-05-06T06:58:03Z

‎Alignment of BESA and MRICoordinate Systems

Robert: /* Define a Dipole in BESA Research at a Location Defined in the MRI */

2021-05-06T06:57:08Z

‎Define a Dipole in BESA Research at a Location Defined in the MRI

Robert: /* Setting Up Coregistration Using BrainVoyager */

2021-05-06T06:56:22Z

‎Setting Up Coregistration Using BrainVoyager

@@ Line 226: / Line 226: @@
 A double-click at any location in the MRI will define a new source at the corresponding location in the BESA Research head model.
-[[Image:MRI Integration (9).gif ‎]]
+Discrete sources can be also seeded from distributed source analysis result or from overlaid fMRI data.
-=== Coregistration with BrainVoyager after Alignment has been Done ===
+Discrete solution can be also send directly to BESA MRI.
-Alignment between BESA Research and BrainVoyager is only required once for a given BESA Research data set and the corresponding MRI. At a later time, if you want to Co-locate sources between BESA Research and BrainVoyager, perform the following steps in BrainVoyager:
+[[Image:MRI Integration (9).gif ‎]]
-* Load the MRI.
-* Load the head surface mesh (''Meshes/Load Mesh..''.).
-* Load the Coregistration File (''EEG-MEG BESA/Load Surface Points..''.).
-=== Send a Dipole from BESA Research to BrainVoyager ===
+=== Send a discrete solution to BESA MRI ===
-First, start BrainVoyager(QX). This can be done from the BESA Research Source Module by pressing the <span style="color:#3366ff;">'''BrainVoyager '''</span>button. Note that in the Source Module, the ''Options / Preferences / BrainVoyager'' tab allows to define the path to BrainVoyager.
+''This feature requires BESA Research 7.1 or higher.''
-In BrainVoyager, [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done|set up coregistration]].
+The current discrete solution (sources - dipoles) can be exported to BESA MRI (version 3.0 and above). It can be done in two ways:
-In the BESA Research Source Module, highlight the dipole of interest.
+* by pressing the menu entry Save Solution for BESA MRI in the File menu of Source Analysis module (recommended)
-In the BESA Research Source Module, click on the <span style="color:#3366ff;">'''BrainVoyager'''</span> button.
+* by saving the current solution in the File menu of Source Analysis using the Talairach coordinate system.
-Program control will automatically switch to BrainVoyager. The head will be cut at the section corresponding to the dipole of interest.
+The first option is only available if data is [[#How_Coregistration_is_done|coregistered]]. Please note that in this scenario also confidence limits will be exported.
-[[Image:MRI Integration (10).gif‎|200px]]
+When ''Save Solution for BESA MRI'' is pressed the file is saved in the subject's MRI data folder. Afterwards, when the subject's MRI segmentation project is opened, the button ''Load Solution'' can be pressed. The solution that was exported is already preselected. After pressing OK, the solution will be loaded. Note that the solution is automatically transformed to ACPC coordinates if required (depending on the display in BESA MRI).
-Note that the dipoles are visible in both the surface module and in the 2D view:
+=== Coregistration with BrainVoyager after Alignment has been Done ===
-[[Image:MRI Integration (11).gif|400px]]
+[[#Setting Up Coregistration Using BrainVoyager|Alignment between BESA Research and BrainVoyager]] is only required once for a given BESA Research data set and the corresponding MRI. At a later time, if you want to Co-locate sources between BESA Research and BrainVoyager, perform the following steps in BrainVoyager:
-=== Define a Dipole in BESA Research at a Location Defined in the MRI ===
+* Load the MRI.
-First set up coregistration (see chapter [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done|Coregistration with BrainVoyager after Alignment has been Done]]).
+BrainVoyager is now ready for Co-location.
-−
-In the BrainVoyager 2D MRI view, place the mouse over the point at which you would like to define a dipole. Right click at this point. If this point lies within an fRMI cluster, BrainVoyager will automatically determine its center and use it as a seeding point instead. Press <span style="color:#3366ff;">'''Send Seed Point To BESA....'''</span>
-−
-[[Image:MRI Integration (12).gif ‎]]
-−
-The following Dialog is opened:
-−
-[[Image:MRI Integration (13).gif ‎]]
-−
-Press <span style="color:#3366ff;">'''Send to BESA'''</span><span style="color:#3366ff;"><span style="color:#00000a;">.</span></span>
-−
-The BESA Source Analysis window appears. The new dipole or regional source (depending on the setting in the ‘Options’ dialog in the Source Analysis window is now displayed at the corresponding location. If a dipole is seeded, BESA automatically fits its orientation. For further adjustment of the model, you may need to refit the orientation, e.g. at a certain time range, or in the presence of other sources.
-−
-Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [http://brainvoyager.com/Downloads.html BrainVoyager Downloads].
 == Reference ==

@@ Line 58: / Line 58: @@
 * After aligning the EEG / MEG and the MRI data it is possible to co-locate dipoles and MRI locations. This means, it is possible to visualize the dipoles and to specify the dipole parameters in the MRI coordinate system.
 * [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module|How to Co-locate sources and MRI in the BESA Research Source Module]] describes how in the BESA Research Source Analysis module dipoles can directly be visualized in the space of the individual MRI.
-* [[Integration_with_MRI_and_fMRI#Send_a_Dipole_from_BESA_Research_to_BrainVoyager|How to Send a Dipole from BESA Research to BrainVoyager]] describes how to send a source model from BESA Research to BrainVoyager for further inspection.
+* [[Integration_with_MRI_and_fMRI#Send_a_Dipole_from_BESA_Research_to_BrainVoyager|How to Send a discrete Solution to BESA MRI]] describes how to export the current solution to the co-registered MRI and open it in BESA MRI.

@@ Line 11: / Line 11: @@
 Both for developing and evaluating dipole source models of EEG or MEG activity, it is useful to have access to structural MRI or fMRI data.
-The BESA MRI software allows to preprocess structural MRI data so that the individual anatomical information contained in the MRI can be utilized in BESA Research. BESA MRI makes it possible ...
+The BESA MRI software allows to preprocess structural MRI data so that the individual anatomical information contained in the MRI can be utilized in BESA Research.
-* ... to align the EEG and MEG sensors with the structural MRI data.
-* ... to read and display the aligned, individual Talairach structural MRIs directly in the BESA Research Source Analysis module. In this way, source analysis results can be presented on top of the aligned MRIs, which allows us to evaluate the anatomical regions to which the reconstructed sources may correspond.
-* ... to use an individual, realistically shaped FEM head model for source analysis in BESA Research. FEM head models take into account the individual volume conduction properties of the subject's head derived from the structural MRI data. This allows for more accurate source analysis (Yvert 1997, Lanfer 2012).
-To offer an easy integration with fMRI data we have, in collaboration with Rainer Goebel, optimized the interface between BESA Research and BrainVoyagerQX.
-With these tools, we can ...
+BESA MRI makes it possible ...
-* ... use fMRI BOLD regions or MRI structures to initialize dipole models.
-* ... visualize dipoles from BESA Research models together with the structural MRI in BrainVoyager in order to evaluate the regions to which the dipoles may correspond.
-* ... combine the localization advantages of (f)MRI with the high temporal resolution of EEG and MEG, for instance by using (f)MRI to place the sources, and the source waveforms of BESA Research to provide feedback about the time course of the source activity.
-* ... overlay source analysis results obtained in BESA Research with fMRI data.
-'''Note:''' For simpler coregistration, we recommend to use BrainVoyagerQX rather than the older BrainVoyager, but BESA Research will work with both program versions.
+*... to read and display the aligned, individual Talairach structural MRIs directly in the BESA Research Source Analysis module. In this way, source analysis results can be presented on top of the aligned MRIs, which allows us to evaluate the anatomical regions to which the reconstructed sources may correspond.
-The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [https://www.brainvoyager.com/downloads/downloads.html BrainVoyager Downloads].
+*... to use an individual, realistically shaped FEM or BEM head model for source analysis in BESA Research. FEM and BEM head models take into account the individual volume conduction properties of the subject's head derived from the structural MRI data. This allows for more accurate source analysis (Yvert 1997, Lanfer 2012).
@@ Line 52: / Line 59: @@
 * [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module|How to Co-locate sources and MRI in the BESA Research Source Module]] describes how in the BESA Research Source Analysis module dipoles can directly be visualized in the space of the individual MRI.
 * [[Integration_with_MRI_and_fMRI#Send_a_Dipole_from_BESA_Research_to_BrainVoyager|How to Send a Dipole from BESA Research to BrainVoyager]] describes how to send a source model from BESA Research to BrainVoyager for further inspection.

← Older revision		Revision as of 07:06, 6 May 2021
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	'''Note:''' For simpler coregistration, we recommend to use BrainVoyagerQX rather than the older BrainVoyager, but BESA Research will work with both program versions.		'''Note:''' For simpler coregistration, we recommend to use BrainVoyagerQX rather than the older BrainVoyager, but BESA Research will work with both program versions.

−	The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website ([https://www.brainvoyager.com/downloads/downloads.html BrainVoyager - Downloads]).	+	The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [https://www.brainvoyager.com/downloads/downloads.html BrainVoyager Downloads].

@@ Line 269: / Line 269: @@
 The BESA Source Analysis window appears. The new dipole or regional source (depending on the setting in the ‘Options’ dialog in the Source Analysis window is now displayed at the corresponding location. If a dipole is seeded, BESA automatically fits its orientation. For further adjustment of the model, you may need to refit the orientation, e.g. at a certain time range, or in the presence of other sources.
-Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website ([http://brainvoyager.com/Downloads.html http://brainvoyager.com/Downloads.html]).
+Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [http://brainvoyager.com/Downloads.html BrainVoyager Downloads].
 == Reference ==

@@ Line 201: / Line 201: @@
 * The brain surface generation is performed as one work step of the BESA MRI segmentation workflow.
 * The cortex surface reconstruction is done using a robust and accurate automatic segmentation procedure.
-* Details on how to generate the brain surface mesh in BESA MRI can be found in the coregistration quickguide which is available on the BESA homepage (http://www.besa.de/downloads/quick-guides/).
+* Details on how to generate the brain surface mesh in BESA MRI can be found in the coregistration quickguide which is available on the BESA homepage: [http://www.besa.de/downloads/quick-guides/ Quick Guides].
@@ Line 208: / Line 208: @@
 * The result of the BrainVoyager procedure is two meshes, one for the left and one for the right hemisphere.
 * BESA Research requires a single mesh. Therefore, load first one mesh (''Meshes/Load Mesh..''.), and append the other mesh (''Meshes/Add Mesh...''). Merge these two meshes (''Meshes/Merge'' ''meshes in surface window'') and then save the result (''Meshes/Save Mesh...''). If possible, use the recommended name conventions for the resulting file (file name ends in "<span style="color:#ff9c00;">'''_TAL_WM.srf"). '''</span>For instance, if the Talairach MRI is named "<span style="color:#ff9c00;">'''MRI PB_TAL.vmr'''</span>", name the brain surface mesh "<span style="color:#ff9c00;">'''MRI PB_TAL_WM.srf'''</span>".
-* See also the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website (http://brainvoyager.com/Downloads.html).
+* See also the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [http://brainvoyager.com/Downloads.html BrainVoyager Downloads].
 ==  Co-locating Dipoles and MRI Locations ==

← Older revision		Revision as of 06:58, 6 May 2021
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−	The alignment steps need only be performed once for a given MRI and EEG/MEG data set. Otherwise, after starting BrainVoyager, just load the MRI, the surface mesh, and the surface points (see “[[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done \|How to Set Up Coregistration with BrainVoyager after Alignment has been Done]]”). Now the following actions are possible: see chapters	+	The alignment steps need only be performed once for a given MRI and EEG/MEG data set. Otherwise, after starting BrainVoyager, just load the MRI, the surface mesh, and the surface points (see [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done \|How to Set Up Coregistration with BrainVoyager after Alignment has been Done]]). Now the following actions are possible: see chapters

	* [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module\|How to Co-Locate Sources and MRI in the BESA Research Source Module]]		* [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module\|How to Co-Locate Sources and MRI in the BESA Research Source Module]]

@@ Line 121: / Line 121: @@
 * BESA Research. Start the ''Coregistration Dialog''. Export the Coregistration File (head surface points) from your data by pressing the<span style="color:#3366ff;"> '''BrainVoyagerQX'''</span> button in the dialog. Save the file to the directory where your MRI is located. BrainVoyagerQX is started.
-* BrainVoyagerQX. Load the MRI corresponding to the EEG/MEG data. For optimal performance, the MRI should be cleaned so that regions outside the head are black. Prepare an AC-PC-transformed MRI and a Talairach MRI. For each, generate a surface mesh. Save these files following our recommended naming conventions (see chapter “[[Integration_with_MRI_and_fMRI#MRI_file_Name_Conventions|MRI File Name Conventions]]”). Save the Talairach coordinate file (<span style="color:#ff9c00;">'''<nowiki>*.tal</nowiki>'''</span>). If these steps have already been performed, load the ACPC MRI and load the ACPC mesh. If you want to generate a brain surface mesh, see chapter “[[Integration_with_MRI_and_fMRI#How_to_Generate_a_Brain_Surface_Mesh|How to Generate a Brain Surface Mesh]]”.
+* BrainVoyagerQX. Load the MRI corresponding to the EEG/MEG data. For optimal performance, the MRI should be cleaned so that regions outside the head are black. Prepare an AC-PC-transformed MRI and a Talairach MRI. For each, generate a surface mesh. Save these files following our recommended naming conventions (see chapter [[Integration_with_MRI_and_fMRI#MRI_file_Name_Conventions|MRI File Name Conventions]]). Save the Talairach coordinate file (<span style="color:#ff9c00;">'''<nowiki>*.tal</nowiki>'''</span>). If these steps have already been performed, load the ACPC MRI and load the ACPC mesh. If you want to generate a brain surface mesh, see chapter [[Integration_with_MRI_and_fMRI#How_to_Generate_a_Brain_Surface_Mesh|How to Generate a Brain Surface Mesh]].
 * BrainVoyagerQX. Load the Coregistration File (''EEG-MEG BESA/Load Surface Points''). The points will be displayed, but they are not aligned to the head: