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.

Go to slice view (S) and toggle (R) the slices until you've chosen the functional map
Go back to the main menu. Change the color coding to spectral by going to Color Coding (C) and Spectral (S). Adjust the color bar so that it encompasses the entire range of data.
Go back to the main menu. Change the background to be transparent by going to Color Coding (C) and Under Color (Z). Type in "transparent" or "0 0 0 0" when prompted.
Go back to the main menu. Make the structural scan visible by going to Slice View (S) and toggling (R) to the structural image. Adjust the color bar until you have good constrast between the gray matter and csf border.
Go back to the main menu. Make the backgroun of the structural scan transparent by going to Color Coding (C) and Under Color (Z). Type in "transparent" or "0 0 0 0" when prompted.
Go back to the main menu. Now we will overlay the functional map onto the structural. Go to Slice View (S) and toggle the Current Volume (T). While hovering the mouse pointer over each view (sagittal, axial, coronal), hit Toggle Slice Visible (S).

You should now see your activation map over the structural scan

3) Slicing the surface to see subcortical activations.

Color Code the object by going to Color Coding (D) and Color Code Object (A).
On the surface, select the point at which you want to make the bottom part of your slice. While hovering the cursor over the plane (axial, sagittal, coronal) you want to make your slice, go to Surface Segmentation (X) and select Crop Below (T). This will remove everything on the surface below your cursor.
On the surface, click on the point at which you want the top part of your slice to be. While hovering the cursor over the plane (axial, sagittal, coronal) you want to make your slice, go to Surface Segmentation (X) and select Crop Above (R). This will remove everything on the surface above where your cursor is.
While your cursor is still on the top part of the slice you just made, add the MRI slice to the picture by going to Slice View (S) and Create 3D Slice (A). This will add the MRI slice onto your sliced surface.