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| == Important notes == * In all the tutorials, we will consider that you are working with the source distribution of Brainstorm, as it is the recommanded way to use this toolbox. If you are working with compiled binaries, some menus might be missing, but everything else should work the same way. * Before starting using Brainstorm with your own data, you should go through __all __the tutorials in "Getting started with Brainstorm" section. In just a few hours, they will introduce you to most of the main features of the application. |
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| <<TableOfContents>> | * If you want a printed version of this documentation: * Open a tutorial, go to the menu on top of the page, * Select ''More actions > Print view'', print the page, * Click on the ''Back ''button of your browser, and go to next tutorial. == Getting started with Brainstorm == === Dataset description === The dataset that will be used for tutorials #2 to #10 is a somatotopy experiment recorded with a CTF 151 MEG system. Please download bst_sample_ctf.zip from the [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] section. Unzip it in a folder you will dedicate to original data. It can be anywhere but __not__ in the Brainstorm database or program folder. Example: * __Windows__: My documents\MEG\sample_ctf\ * __Linux__: /home/username/MEG/sample_ctf/ * __MacOS__: Documents/MEG/sample_ctf/ ||<width="150px" style="vertical-align: top;">File: ||'''bst_sample_ctf.zip''' || ||<style="vertical-align: top;">Acquisition system: ||CTF MEG, 151 axial gradiometers, La Salpetriere Hospital, Paris || ||<style="vertical-align: top;">Protocol: ||Shuffled electrical stimulations of the thumb fingers from both hands. The idea is to get a map of the primary sensory response on the cortex || ||<style="vertical-align: top;">Author: ||Data provided courtesy of Sabine Meunier || ||<style="vertical-align: top;">Anatomy directory: ||- T1-MRI of the subject in CTF format (.mri).<<BR>>- Cortex and head surfaces extracted with BrainVISA software([[Tutorials/SegBrainVisa|see tutorial]]) || ||<style="vertical-align: top;">Datasets directory: ||- somMGYO-18av.ds: average response for the stimulation of the right thumb (one subject, 400 trials) .<<BR>>- somMDYO-18av.ds: average response for the stimulation of the left thumb (one subject, 400 trials) || ||<style="vertical-align: top;">Observations: ||Stimulus occurs at time 0. There's a first tiny wave occuring at about 20ms or so but it's not too clear on all fingers. So if you are to compute cortical maps, start by the 40ms peak which is also of interest and which has much better SNR. || === Step by step tutorials === * [[Tutorials/BstFolders|0. Introduction to Brainstorm structure]] * [[Tutorials/TutFirstSteps|1. First steps]] * [[Tutorials/TutImportAnatomy|2. Importing individual anatomy]] * [[Tutorials/TutImportRecordings|3. Importing recordings]] * [[Tutorials/TutExploreRecodings|4. Exploring the recordings]] * [[Tutorials/TutHeadModel|5. Computing a head model]] * [[Tutorials/TutNoiseCov|6. Computing a noise covariance matrix]] * [[Tutorials/TutSourceEstimation|7. Source estimation]] * [[Tutorials/TutScouts|8. Scouts: cortical regions of interest]] * [[Tutorials/TutProcesses|9. Processes: Graphical batching interface]] == Other useful tutorials == 1. [[Tutorials/SegBrainVisa|Extract head and cortex surface with BrainVISA]] 1. [[Tutorials/SegBrainSuite|Extract head and cortex surface with BrainSuite]] 1. [[Tutorials/SegFreeSurfer|Extract head and cortex surface with FreeSurfer]] 1. [[Tutorials/TutInverseExpertMode|More inverse methods]] 1. [[CiteBrainstorm|Cite Brainstorm in your publications]] |
Tutorials
Important notes
- In all the tutorials, we will consider that you are working with the source distribution of Brainstorm, as it is the recommanded way to use this toolbox. If you are working with compiled binaries, some menus might be missing, but everything else should work the same way.
Before starting using Brainstorm with your own data, you should go through all the tutorials in "Getting started with Brainstorm" section. In just a few hours, they will introduce you to most of the main features of the application.
- If you want a printed version of this documentation:
- Open a tutorial, go to the menu on top of the page,
Select More actions > Print view, print the page,
Click on the Back button of your browser, and go to next tutorial.
Getting started with Brainstorm
Dataset description
The dataset that will be used for tutorials #2 to #10 is a somatotopy experiment recorded with a CTF 151 MEG system.
Please download bst_sample_ctf.zip from the Download section. Unzip it in a folder you will dedicate to original data. It can be anywhere but not in the Brainstorm database or program folder. Example:
Windows: My documents\MEG\sample_ctf\
Linux: /home/username/MEG/sample_ctf/
MacOS: Documents/MEG/sample_ctf/
File: |
bst_sample_ctf.zip |
Acquisition system: |
CTF MEG, 151 axial gradiometers, La Salpetriere Hospital, Paris |
Protocol: |
Shuffled electrical stimulations of the thumb fingers from both hands. The idea is to get a map of the primary sensory response on the cortex |
Author: |
Data provided courtesy of Sabine Meunier |
Anatomy directory: |
- T1-MRI of the subject in CTF format (.mri). |
Datasets directory: |
- somMGYO-18av.ds: average response for the stimulation of the right thumb (one subject, 400 trials) . |
Observations: |
Stimulus occurs at time 0. There's a first tiny wave occuring at about 20ms or so but it's not too clear on all fingers. So if you are to compute cortical maps, start by the 40ms peak which is also of interest and which has much better SNR. |
Step by step tutorials
?0. Introduction to Brainstorm structure
?1. First steps
?2. Importing individual anatomy
?3. Importing recordings
?4. Exploring the recordings
?5. Computing a head model
?6. Computing a noise covariance matrix
?7. Source estimation
?8. Scouts: cortical regions of interest
?9. Processes: Graphical batching interface