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Back to Tutorial Top
Back to Multimodal Top

Other Multimodal Tutorials: B. Individual DTI Integration, C. Individual fMRI Integration, D. Surface-based Group fMRI Analysis,


The purpose of this tutorial is to get you acquainted with the concepts need to perform multi-modal integration in FreeSurfer using fMRI and DTI analysis. You will not learn how to perform fMRI or DTI analysis here; that knowledge is already assumed. The fMRI makes use of data from the Functional Biomedical Informatics Research Network (fBIRN, www.nbirn.net).

1. Preparations

1.1. If You're at an Organized Course

If you are taking one of the formally organized courses, everything has been set up for you on the provided laptop. The only thing you will need to do is run the following commands in every new terminal window (aka shell) you open throughout this tutorial. Copy and paste the commands below to get started:

setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101

To copy: Highlight the command in the box above, right click and select copy (or use keyboard shortcut Ctrl+c), then use the middle button of your mouse to click inside the terminal window (this will paste the command). Press enter to run the command. These two commands set the SUBJECTS_DIR variable to the directory where the data is stored and then navigates into this directory. You can now skip ahead to the tutorial (below the gray line).

1.2. If You're not at an Organized Course

If you are NOT taking one of the formally organized courses, then to follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. These are the commands that you need to run before getting started:

source your_freesurfer_dir/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101

Notice the command to open tcsh. If you are already running the tcsh command shell, then the 'tcsh' command is not necessary. If you are not using the tutorial data you should set your SUBJECTS_DIR to the directory in which the recon(s) of the subject(s) you will use for this tutorial are located.

2. Basic Manual Registration

The purpose of this exercise is to:

  1. Familiarize you with the FreeView and/or tkregister2 command interface.

  2. Show you how to make manual adjustments to the registration.
  3. Show you what a bad registration is and how hard it is to fix manually.

Option A: In order to use FreeView, run the command below:

freeview -v template.nii \
$SUBJECTS_DIR/fbirn-anat-101.v4/mri/orig.mgz:visible=0 -f \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/lh.white:edgecolor=green \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/rh.white:edgecolor=green \
-viewport coronal

This should bring up an interface that looks like this:

FreeView.Snap1.sm.png FreeView.Snap2.png FreeView.Snap3.png

  1. The gray scale image is the functional.
  2. The green line is the white surface.
  3. Gray matter and CSF are bright while white matter is dark.

Notice how the surfaces do not line up with the anatomy in the functional volume. You can turn the orig volume on and off to see how much the registration is off. To do manual registration in FreeView, select the volume you want to adjust (in this case, choose template) and then go to the 'Tools' menu and select 'Transform Volume'. Hit 'OK' to the warning that pops up. Select the 'Translate' tab and play around with the sliders until the surfaces follow the anatomy better. You could play with the Rotation, as well. When you are happy with your results, save the registration file and/or the resampled volume. If you would like to start over, you can choose 'Restore to Original'. Note, FreeView will save .lta type registration files.

Option B: In order to use tkregister2 for this task, load a functional volume with the anatomical volume using:

tkregister2 --mov template.nii --s fbirn-anat-101.v4 \
 --regheader --reg myregister.dat --surf

The FreeSurfer subject name is "fbirn-anat-101.v4". --regheader indicates that tkregister2 should assume that the volumes are already in registration. myregister.dat is the output registration (does not exist yet). This should bring up an interface that looks like this:

Things to do:

  1. Click in the image window and hit the 's' key to toggle the surface on and off.
  2. Click on the "COMPARE" button to toggle between the functional and the anatomical. Note that the green surface is aligned with the anatomical.
  3. Change orientation by clicking on the "CORONAL", "SAGITTAL", and "HORIZONTAL" buttons.
  4. NOTE: DO NOT SPEND MORE THAN 5min DOING THIS STEP! Attempt to register the functional manually by adjusting the "TRANSLATE BRAIN" and "ROTATE BRAIN" sliders. Do NOT use "SCALE BRAIN".
  5. You can hit the "SAVE REG" button at any time to save a registration. (This will save a .dat type registration file.) If you hit it again, it will ask you if it is ok to overwrite it (it is).

3. Automatic Registration

The purpose of this exercise is to show you how to use the automatic registration program (bbregister). To run, cut and paste this command into your shell:

  bbregister --mov template.nii --bold \
    --s fbirn-anat-101.v4 \
    --init-fsl --lta register.lta


  1. --bold indicates that the template has bold/T2 contrast (meaning that gray matter is brighter than white matter).
  2. --init-fsl indicates that the program should use FSL FLIRT. You must have FSL installed.

  3. --lta indicates that the output registration file is register.lta (Note, currently register.dat will also be written into the output directory for backwards compatibility.)
  4. This will take about 5 min (the same amount of time you spent manually, right?)

4. View Automatic Registration

Look at the register.dat text file created:

cat register.lta

Click here to see an example.

In order to load a functional volume with the anatomical volume specifying the recently created automatic registration:

Option A: Using FreeView

freeview -v $SUBJECTS_DIR/fbirn-anat-101.v4/mri/orig.mgz \
template.nii:reg=bb.register.lta -f \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/lh.white:edgecolor=green \
$SUBJECTS_DIR/fbirn-anat-101.v4/surf/rh.white:edgecolor=green \
-viewport coronal

Select the template volume and hit Alt+v to switch between the template and orig or change the opacity value on the top volume to observe the quality of the alignment. See how much better the registration is now? How does it compare to your manual registration?


Option B: Using tkregister2

tkregister2 --mov template.nii --reg register.dat --surf


  1. The subject is not specified since it is in the register.dat
  2. --regheader is not used

How does this registration look compared to your manual registration above? Can you make it any better?

Other Multimodal Tutorials: B. Individual DTI Integration C. Individual fMRI Integration, D. Surface-based Group fMRI Analysis

FsTutorial/MultiModalRegistration_freeview (last edited 2017-03-23 20:22:33 by AndrewHoopes)