Brain Voyager

Go to Volume → 3D Volume tools Go to Spatial Trans. Click on 'To Sag' under standardise You can now manually transform the image to sagittal view (looking at the face side-on with nose pointing to the left – see image in results) Under FMR-VMR coregistration select FMR and then click on Align There are two stages to the coregistration – The Initial Alignment (IA) and the Fine Tuning Alignment (FA). You can either let BrainVoyager try to do this automatically or do it manually. For automatic coregistration click Run. For manual Initial Alignment Click on the 'use SAG matrix' option, and manually align the images for the FA stage.
 * 1) Create new functional MRI project using project wizard.  Go to Project wizard, FMR project and specify the data
 * 2) Pre-process the functional data Go to Analysis → FMR Data Preprocessing Expand menu by clicking on Advanced Default of Slice scan time correction, 3D motion correction and temporal filtering used, parameters changed as necessary i.e. voxel size, TR, slice sequence etc
 * 3) Create new anatomical MRI project using project wizard Go to Project wizard, VMR project and specify the data, the data may be resized once loaded
 * 4) Spatially transform image to sagittal view (only if it is not in sagittal view already)
 * 1) Coregister anatomical and functional images – This did not work well so manually aligned the images using my defined sagittal transformation and placement Go to Coregistration
 * 1) Normalise to Talairach space

Go to the Talairach tab

Firstly normalise the data to ACPC space by identifying the Anterior Commissure and rotating the image to the ACPC plane (click on the relevant buttons to do this), run this

Then define further points for Talairach normalisation (there is a list of points to define, the first says AC for Anterior Commissure). You also need to specify PC (posterior commissure). Be careful when specifying the left and right sides of the brain as in radiological convention left is on the right and right is on the left …

7. Create a 3D-aligned time course (VTC) file to apply same parameters to functional data,

Go to analysis and select 'Create 3D aligned time course (VTC) data'

Select the fMR project

Select the outputs from the coregistration in the appropriate places

Click on 'To Tal' at the top to ensure the data are aligned to Talairach space

Select the files from ACPC and Talairach alignment which are asked for

Click on 'Go'

Go to analysis and select 'Link 3D time-course file' then select the VTC file

8. Go to analysis and click on 'VTC data Preprocessing'

Smooth and (optionally) temporal filter the data, change the TR and the FWHM of the smoothing kernel as necessary

9. Defining the task and applying the GLM

Go to analysis → stimulation protocol and specify the conditions for your task, save the file

Go to analysis → General Linear Model: Single study, click on 'Define Preds' and 'Go' to estimate parameters

Go to analysis → Overlay General Linear Model to get on image

Go to analysis → Overlay Volume Maps to get thresholding and presentation options

To get a table of results:

1. When the 'Overlay Volume Maps' is open, under 'Statistics' and then under 'Cluster threshold', click on 'Enable' and specify a minimum number of voxels for each cluster in box underneath

2. Go to options → Convert Map Clusters to VOIs and select whether to have a VOI for each cluster or one VOI for all active voxels, change the cluster threshold if you want and click 'Go'

3. A new window will pop up, click on 'Options' along the bottom of the window, select the tab 'VOI functions' and under Map Peak Voxels click on 'Table' and a results table will be produced

Group Analysis

1. Go to Analysis → General Linear Model: Multi Study, Multi Subject

2. Click on RFX GLM to get a random effects analysis

3. Click on 'Add to List' and select a dataset, repeat this until all data have been selected

4. Click on 'Go'

5. Overlay as before
 * 1) Numbered list item
 * 1) Numbered list item