Neuroimaging Made Easy : windows

Showing posts with label windows. Show all posts

Tuesday, 22 November 2011

Brainvoyager QX tips and tricks 2; Create a 3d shape by drawing a region of interest

In the following slides, I will present a simple method of creating a 3d mesh from a region of interest using draw with mouse tool.

First of all, open any *.vmr file, when you click on 3D volume tools, choose segmentation tab as shown in the following image. Tick enable for draw with mouse option (I selected 2D in-plane) because I drew a region of interest around corpus callosum. If you want to draw a multislice volume you can choose 3D (cube) but with care as you move from slide to another. To change draw tool color you should change (New) value in rage (225-240). I got orange color by change value to 226.

You can start drawing by selecting (ctrl+left click in windows) and (cmd+mouse left click in MAC).

After finishing drawing, click on 3D volume tools then choose segmentation tab and option as shown in the following image. Next steps are shown in the following series images.

Then select mesh morphing to smooth resulted shape.

In the final step, we save resulted mesh

We can combine two meshes by adding another mesh as shown in the following image.

Run multiple BrainVoyager instances on Mac OSX

Create an averaged brain in Brainvoyager QX

Brainvoyager QX; rename DICOM files in multiple folders at once

Autoscale of vmr files (Brainvoyager QX) & automation of Advanced segmentation tools

Monday, 21 November 2011

Brainvoyager QX tips and tricks 1; Some visualization tips

This entry is part of my talk about advanced features of visualization in Brain Voyage QX which was held in May 2008 at MARIARC, Liverpool.

I used BVQX (1.9.10). There are some differences between different versions, so please take this issue in account if you use another version. Hopefully, this could help!

Before starting; you have to refer to BrainVoyager QX Getting Started Guide
BrainVoyager QX Getting Started Guide

1- Sphere Mapping (Cortex-based alignment)

This can be done faster and easier in an automated way using a script provided through brain voyager QX support site by Draulio de Araujo. However, I am showing the normal method here.

2- Illustration of Brodmann areas, lobes, sulcus and gyruses...(on mesh)

Sphere Mapping should be processed before starting this step. Doing all of the previous steps ending with folding the (...RECOSM.srf) mesh by setting standard sphere vertices (image 7).

You should load a patch of interest from database that located in Atlas Brains folder in Brain voyager QX directory.

3- Illustration of Brodmann areas on 3D view; SAG, COR, AND TRA

You should download brodma.voi from Brain voyager user forums. or email me if you want a copy. (This file is available in the newest versions (Brainvoyager QX 2.x.x).

4- Drawing region on a mesh

In the following step, you should use ctrl and mouse click in order to draw a region of interest.When you finish drawing a closed curve you can toggle to fill mode and fill the region.

5- Representation of demarcated region on a polygon mesh

Run multiple BrainVoyager instances on Mac OSX

Create an averaged brain in Brainvoyager QX

Brainvoyager QX; rename DICOM files in multiple folders at once

Autoscale of vmr files (Brainvoyager QX) & automation of Advanced segmentation tools

Sunday, 20 March 2011

Create an averaged brain in Brainvoyager QX

Regional differences in sulcal and gyral topography can be used as disease indications such as in schizophrenia (Csernansky et al., 2008). In the previous video I showed how we can combine multiple aligned surfaces (.srf files) in one surface brain like the following image;