Functional MRI and Display

This page describes how to register a functional image from FSL to the CCB surface. It also describes how to slice the surface so that subcortical activations can be visualized.

Step 1: Registering the FSL functional output to the CCB brain

1) Get a copy of the get_threshmap_to_CCB.csh from /loni/edevel/bin/ERIC_CODE.
This script assumes that the functional map has been registered to the avg132T1_brain that is the standard template for FSL. If this is true, then running the script with the avg152T1_brain_305 as the fmri_struct is correct. If this is not true, you will need to take the template that FSL used and transform it to 305 space first, as well as extract a surface for it.

2) The only values in the script that need to be changed are the variables at the beginning of the script
The idea of this script is to register the functional maps to CCB space by registering the template the functional maps were aligned to to CCB space. Once we get the transformation file for the template -> CCB space we can then apply that same transform to our functional maps.

Please read the comments in the script for further explanation of what each step does.

Step 2: Visualizing the data in Display

1) Open the files in Display
Display CCB_305.mnc (your functional map).mnc CCB_305.obj

2) Overlay the functional map on the structural scan.

You should now see your activation map over the structural scan

3) Slicing the surface to see subcortical activations.