= Using BrainVISA =
''Authors: Francois Tadel''

It is not the purpose of Brainstorm tutorials to teach you how to use BrainVISA. But many Brainstorm users are lost when it gets to the segmentation of the MRI. So here is a short introduction to the BrainVISA T1 MRI processing pipeline. To extract head and cortex meshes from a T1 MRI, you can also try to use: [[Tutorials/SegBrainSuite|BrainSuite]] or [[Tutorials/LabelFreeSurfer|FreeSurfer]].

We are going to illustrate the use of BrainVISA with the MRI from the CTF tutorials. You should already have these files on your computer, if you followed the basic tutorials. If it is not the case, go to the [[http://neuroimage.usc.edu/bst/download.php|Download page]], and get the file sample_ctf.zip.

This tutorial was written for BrainVISA 4.3. To get started, or for additional information, you can also read the [[http://brainvisa.info/doc/axon/bv_training/en/html/index.html|BrainVISA tutorial pages]].

<<TableOfContents(2,2)>>

== Installation ==
 * Download the latest version of BrainVISA from http://brainvisa.info
 * Install it on your computer by following the instructions on the [[http://brainvisa.info/download.html#installation|download page]].
 * Start BrainVISA
 * You have to create a database for storing your files: this will be either asked at startup, or you'll have to select the menu BrainVISA > Preferences: <<BR>><<BR>> {{attachment:database.gif}} <<BR>><<BR>>

 * Click on Add, and create a directory with is __not__ in any Brainstorm directory. For example:
  * '''Windows''': My Documents\brainvisa_db\
  * '''Linux''': /home/username/brainvisa_db/
  * '''MacOS''': Documents/brainvisa_db/
 * Click on Ok.

 * Your are ready to import and process your MRI.

== Running BrainVISA ==
==== Start Morphologist ====
The T1 MRI processing pipeline in BrainVISA is now called Morphologist. Double-click on the icon "Morphologist 2012" to get started.

{{attachment:morphologist.gif}}

The Morphologist window shows on the left the list of analysis steps that are part of this T1 MRI processing pipeline. They can be selected or unselected independently. When you click on a step, it shows all the possible options and input and output files on the right.

{{attachment:morphologist2.gif|morphologist.gif}}

==== Select the MRI file ====
The only options than we need to set (hopefully), are the global ones, that you get when you click on the top element in the list (Morphologist 2012). Let's start with the selection of the MRI file:

 * On the "mri" line, click on the button that says "Browse the filesystem (load mode)", the last one on the line, that represents a folder. The other button, the green one, is for selecting a subject that is already in the database.
 * Select the tutorial file sample_ctf/Anatomy/'''01.nii'''  <<BR>><<BR>> {{attachment:selectFile.gif|morphologist.gif}}
 * On the "mri_corrected" line, click on the red button that says "Browse the database (save mode)", the second to last one. Enter the following options:<<BR>><<BR>> {{attachment:output.gif}} <<BR>><<BR>>
  * File format: NIfTI-1 image
  * Protocol: segmentation
  * Subject: ctf01
 * Click on ok.

==== Setting the options ====
 * '''Anterior commissure''':
  * Click on the "Anatomist" button (at the end of the line). This will start anatomist.
  * In Anatomist window, look for a view that gives you an axial view
  * Then place the cross on the anterior commissure (see page: CoordinateSystems)
  * Go  back to the "T1 Pipeline" window again, and click again on "Anatomist"  button for the anterior commissure. This should write the current  position of the cursor in the "Anterior commissure" field. <<BR>><<BR>> {{attachment:anatomist.gif|output.gif}} <<BR>><<BR>>
 * '''Posterior commissure''': Same operation
 * '''Interhemispheric point''': Same operation, pick it on the top part of the brain.
 * '''Left hemisphere point''':  Same, but be VERY carful with this. By default, contrary to Brainstorm,  the view in Anatomist is in radiological convention. Which means that  the left point you have to pick is shown '''on the right part on the axial slice'''.
  * If  for some reason the MRI you are importing has the left and right  flipped, you should click on the left part of the axial slice, and then  set the option "allow_flip_initial_MRI" to "true" in the "AC/PC step".
 * Keep all the other options to their default values.
 * Just '''uncheck '''the steps: '''Cortical Fold Graph''' and '''Sulci recognition'''. We don't need these two, and they take a lot of time.
 * Click on Run and pray hard. It doesn't take long, but it may crash.<<BR>><<BR>> {{attachment:T1PipelinePrepare.gif|output.gif}}

==== What if if crashes? ====
 * Try changing the options of the process that crashed
 * Post your problem on the BrainVISA forum
 * Try another software, such as [[Tutorials/LabelFreeSurfer|FreeSurfer]]

<<BR>><<BR>>

== Importing the results in Brainstorm ==
 1. Switch to the anatomy side of the database explorer
 1. Create a new subject, set the default anatomy option to "No, use individual anatomy"
 1. Right-click on the subject > Import anatomy folder...<<BR>><<BR>> {{attachment:import1.gif}} <<BR>><<BR>>
 1. Select the file format "BrainVISA folder" and select the top folder of your subject: /.../brainvisa_db/segmentation/ctf01
 1. 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. By default we set this  value to 15000 for the entire brain (it means 7500 for each hemisphere).<<BR>><<BR>> {{attachment:nVertices.gif}} <<BR>><<BR>>
 1. The  MRI Viewer appears, and a help window asks you to validate the  orientation of the MRI and to define the 3 missing fiducial points (NAS/LPA/RPA, as the three others are already imported). If something  doesn't look right at this step, for instance if the MRI is  not  presented with a correct orientation, you should stop this automatic   import process and follow the manual instructions in the basic tutorial   pages. <<BR>><<BR>> {{attachment:mriviewer.gif}} <<BR>><<BR>>
 1. Place the three fiducials NAS/LPA/RPA. If you need help, refer to this page: CoordinateSystems
 1. Click on Save to keep your modifications, and the automatic import will go on.
 1. This process imports the following files from the folder ...'''/ctf01/t1mri/default_acquisition/default_analysis/''' :<<BR>>
  * '''nobias_ctf01.nii.gz'''   (T1 MRI volume)
  * '''ctf01.APC''' (position of the fiducials AC, PC and IH)
  * segmentation/mesh/'''ctf01_head.gii'''    (head surface)
  * segmentation/mesh/'''ctf01_Lhemi.gii'''    (grey/csf interface, left hemisphere)
  * segmentation/mesh/'''ctf01_Rhemi.gii'''    (grey/csf interface, right hemisphere)
  * segmentation/mesh/'''ctf01_Lwhite.gii''' (white matter, left hemisphere)
  * segmentation/mesh/'''ctf01_Rwhite.gii''' (white matter, right hemisphere)
 1. The successive steps that are automatically performed by Brainstorm:
  * Import all the surfaces (left/right, white/cortex)
  * Downsample each hemisphere to the number specified in the options (by default 7500, half of the total default number 15000)
  * Merge left and right hemispheres for the two surface types: white matter and cortex envelope
  * Delete all the unnecessary surfaces
  * Fill the holes in the head surface
 1. The files you can see in the database explorer at the end: <<BR>><<BR>> {{attachment:checkDb.gif}} <<BR>><<BR>>
  * '''MRI''': The T1 MRI of the subject
  * '''ctf01_head_8000V''': Scalp surface generated by Brainvisa (holes filled by Brainstorm).
  * '''cortex_70000V''': High-resolution cortex surface that was generated by BrainVISA.This one  appears in green, it means that is going to be used as the default by  the processes that require a cortex surface.
  * '''cortex_15000V''': Low-resolution cortex surface, downsampled using the '''reducepatch''' function from Matlab (it keeps a meaningful subset of vertices from the original surface).
  * '''white_70000V''': High-resolution white matter envelope from BrainVISA
  * '''white_15000V''': Low-resolution white matter, processed with reducepatch
 1. 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.<<BR>><<BR>>
  . {{attachment:result.gif}}
 <<BR>><<BR>>

== Handling errors ==
==== How to check the quality of the result ====
It's  hard to estimate what would be a good cortical reconstruction. What 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, just  with a visual inspection. 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  and right were not flipped: right-click on the low-resolution cortex  > MRI registration > Check MRI/surface registration...

{{attachment:checkAlign.gif}}

==== 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 BrainVISA pipeline. The options are:

 * Ask help from the developer through the BrainVISA user forum
 * Use [[Tutorials/LabelFreeSurfer|FreeSurfer]] instead

==== The head surface looks bad ====
It  is not mandatory to have a perfect head surface to use any of the  Brainstorm features: you don't necessarily have to recognize the face  (for the anonymity of the figures, it can be even better if you don't).

The  head surface is important mostly for the alignment of the MEG sensors  and the MRI. If you digitized the head shape with a Polhemus device, you  can 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:  the Polhemus head shape (green points) and the head surface from the MRI  (grey surface). 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.

{{attachment:checkAlignMeg.gif||width="298",height="243"}}

If  the default head surface looks bad, you can try generating another one:  right-click on the subject folder > Generate head surface. The  options are:

 * '''Number of vertices''':  Number of points that are kept from the initial isosurface computed from  the MRI. Increasing this number may increase the quality of the final  surface.
 * '''Erode factor''': 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.
 * '''Fill holes factor''':  Number of dimensions in which the holes should be identified and  closed. Increasing this number removes more of the cavities of the head  surface (0=no correction, 1=removes holes inside the surface, 3=closes  all the features that make the surface non-convex)<<BR>><<BR>> {{attachment:generateHead.gif}}

You can also try to import manually the original BrainVISA head surface. Right click on the subject > Import surface > ctf01_head_8000V. If the surface has holes, you can right-click on the head surface > Fill holes, and then use a different value than the one used by default in the automatic procedure (2).

== Cortical parcellations ==
The default analysis pipeline in BrainVISA implements an automatic parcellation of the cortical surface in anatomical regions. The '''MarsAtlas''' model is described here: https://meca-brain.org/software/marsatlas/

This atlas is available only on the grey-white interface (surface file white_*). It is imported in Brainstorm as scouts (cortical regions of  interest), and saved directly in the surface files. To check where they  are saved: right-click on the low-resolution white surface > File >  View file contents. You can see the available structures "Atlas", the  first one that has Name='User scouts', and the second one  Name='MarsAtlas'.

{{attachment:viewMat.gif}}

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):

{{attachment:marsAtlas.gif}}

== Manual import of the anatomy ==
In case you need to import the MRI, surfaces and atlases separately instead of using the menu "Import anatomy folder", here is the sequence of operations to perform to get to the same result:

 1. From the ''Anatomy'' side of the database explorer: create a subject.
 1. Right-click on the subject folder > Import MRI > Select "nobias_subjectname.nii.gz"
 1. Set the 6 fiducial points, save
 1. Right-click on the subject folder > Import surfaces > Select simultaneously: head.gii, Lhemi.gii, Rhemi.gii, Lwhite.gii, Rwhite.gii
 1. Select Lhemi, Rhemi, Lwhite, Rwhite, right-click > Less vertices > 7500 vertices > Select the first option "Matlab reducepatch"
 1. Select Lhemi, Rhemi, right-click > Merge surfaces: Generates a surface cortex_70000V
 1. Select Lwhite, Rwhite, right-click > Merge surfaces: Generates a surface white_70000V
 1. Select Lhemi_7500V, Rhemi_7500V, right-click > Merge surfaces: Generates a surface cortex_15000V
 1. Select Lwhite_7500V, Rwhite_7500V, right-click > Merge surfaces: Generates a surface white_15000V
 1. Delete all the separate hemispheres: *hemi*, *white*
 1. Double-click on cortex_15000V to set it as the default cortex

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