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Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version and. Downloading and installing FreeSurfer is very easy. It just takes some time because the distribution package is huge (get. This tutorial makes use of the same T1 weighted image dataset (bert) that is used for the FreeSurfer tutorial available at the following location.

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It also registers the individual cortex surfaces to surface-based anatomical atlases Desikan-Killiany, Destrieux, Brodmann. The process is fully automatic and the results can be imported in Brainstorm with just a few mouse clicks. It just takes some time because the distribution package is huge get ready to download several Gb.

FsTutorial – Free Surfer Wiki

You have two options: Just follow the instructions: If you’re not sure what csh is: The process is fully automatic, but quite resource-consuming. Everything is ready to be imported in Brainstorm.

The results are usually good, but depending on the quality of the structural MR, it may fail. Because of this unpredictable behavior, you always need to check visually the final surfaces.

The FreeSurfer wiki suggests that you tuorial all the steps with FreeSurfer. More detailed instructions for setting up the environment and tuning the reconstruction here: Then you’re prompted for the number of vertices you want in the final cortex surface. This will by extension define the number of dipoles to estimate during the source estimation process.

Free Surfer

By default we set this value to for the entire brain it means for each hemisphere. If something doesn’t look right at this step, for instance if the MRI is not presented with a correct orientation, freesugfer should stop this automatic import process and follow the manual instructions in the basic tutorial pages.

Place the six fiducials. If you need help, refer to this page: CoordinateSystems Click on Save to keep your modifications, and the automatic import will go on. Scalp surface generated by Tutorlal.

The numbers indicate the parameters that were automatically used for this head: High-resolution cortex surface that was generated by FreeSurfer, that contains usually betweenandvertices. Low-resolution cortex surface, downsampled using the reducepatch function from Matlab it keeps a meaningful subset of vertices from the original surface.

It appears in green in the database explorer, ie. Low-resolution white matter, processed with reducepatch aseg atlas: Atlas of subcortical regions A figure is automatically shown at the end of the process, to check visually that the low-resolution cortex and head surfaces were properly generated and imported.


If it doesn’t look like the following picture, do not go any further in your source analysis, fix the anatomy first. Handling errors How to check the quality of the result It’s hard to estimate what would be a good cortical reconstruction.

Tutoiral you are trying to spot at this level is mostly the obvious errors, like when the early stages of the brain extraction didn’t perform well, tuutorial with a visual inspection.

FsTutorial/Data – Free Surfer Wiki

Play with the Smooth slider in the Surface tab. If it looks like a brain two separate hemispheres in both smooth and original views, it is probably ok. Display the cortex surface on top of the MRI slices, to make sure that they are well aligned, that the surface follows well the folds, and that left freezurfer right were not flipped: The cortex looks bad It is critical to get a good cortex surface for source estimation.

If the final cortex surface looks bad, it means that something didn’t work well somewhere along the FreeSurfer pipeline. You can refer to the following page to fix the problems manually: The head surface looks bad It is not mandatory to have a perfect head surface to use any of the Brainstorm features: If you digitized the head shape with a Polhemus device, you freeeurfer automatically align the head surface hence the MRI with the MEG sensors in the same referential as the Polhemus points.

The quality of this automatic registrations depends on the quality of both surfaces: If you placed lots of points on the nose but your head surface doesn’t have a nose, these points are not going to help. Except for that, a nice head shape is mainly useful for producing nicer figures. If the default head surface ffeesurfer bad, you can try generating another one: Number of points that are kept from the initial isosurface computed from the MRI.

IS&T RCS Tutorial – Introduction to FreeSurfer

Increasing this number may increase the quality of the final surface. Number of pixels to erode after the first binary threshold of the MRI.

Increasing this number removes small components that are connected to the head. Number of dimensions in which the holes should be identified and closed. The description of this feature freesurer available here: To check where they are saved: To access them from the interface: Double-click on the cortex and go to the Scout tab, and click on the drop-down list to select another Atlas ie group of scouts: Desikan-Killiany atlas Displayed respectively in: FreeSurfer, Brainstorm high-resolution and Brainstorm vertices Destrieux atlas Displayed in Brainstorm with the original scouts colors left or classified in 6 regions right: You can switch between the two views with the button “Identify regions with colors” in the toolbar on the right of the scouts list.


Brainstorm reads these volume labels and tesselates some of these freesrufer, groups all the meshes in a large surface file fdeesurfer the regions are identified in an atlas called “Structures”.

It creates a new surface with only the selected regions. If you want to freeesurfer one or several structures, use the menu “Remove selected scouts” instead. Read more about the FreeSurfer subcortical atlas on freesurffr software wiki: There is nothing that can be done with this information at this point, tutorail it will become helpful when projecting the source tutoriall from the individual brains to the default anatomy of the protocol, for a group analysis of the results: Read more about the FreeSurfer registration process on the software wiki: This freesufrer is an average of 40 subjects using a spherical averaging described in Fischl et al.

If it is not available on your computer yet, it will be automatically downloaded from the server to your user folder: If you are using the FSAverage template but not a regular user of FreeSurfer, please register on their website: Running the folder import as a process You can import the FreeSurfer folders from scripts, but you have to provide manually the position for all the fiducial points: The corresponding process function is: From the Anatomy side of the database explorer: In the scout tab: Repeat for the other surfaces: Leave your mouse for a second over the new folder, an note the study index iStudy.

From the Matlab command window, you can import the thickness maps with the following call: Comments, bug reports, suggestions, questions Email address if you expect an answer: Toggle sidebar Toggle navigation.