• 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.

Inspection of Freesurfer Output

In this exercise you will be able to visualize and inspect a good output so that you can become familiar with what the end product should look like. This will step you through visual inspection of a variety of output, but is not necessarily the recommended procedure to take when trying to verify each subject. Some steps are only necessary to check when there are problems, however it is a good idea for new users to become familiar with what the expected output look like and how to view it.

First you need to set your SUBJECTS_DIR to the appropriate place:

cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
setenv SUBJECTS_DIR ${PWD} 

The volumes that are output can be loaded into tkmedit, along with surfaces and the subcortical segmentation. With one command line you can load in the brainmask.mgz and wm.mgz volumes, the rh.white and lh.white surfaces, and the subcortical segmentation.

tkmedit good_output brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white -segmentation aseg.mgz

You should see a tkmedit window open up to this:BR attachment:good_output1.jpg BR

You are currently looking at the brainmask.mgz (loaded as the main volume) with the surfaces displayed and the aseg.mgz (subcortical segmentation) overlayed. The pial (red line), white (yellow line) and orig (green line) surfaces are all shown. You can toggle between the brainmask.mgz (main volume) and the wm.mgz (aux volume) and you can click on and off the aseg.mgz overlay. To become more familar with the buttons in the Tkmedit Toolbox please read the [wiki:FsTutorial/Tools Freesurfer Tools] section of this tutorial.

The things you can look at while this is loaded in tkmedit:

• talairch transformation
• intensity normalization
• skull strip
• wm.mgz volume
• the final surfaces
• subcortical segmentation

For the first run through you might find it easiest to toggle off the aseg with the attachment:icon_seg_volume.gif button.

Talairach transformation

To load in the talairach go to File -> Transforms -> Load Transform for Main Volume and browse to that talairach.xfm file that should be found in the $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/good_output/mri/transforms directory.

When you do this you should see this:

attachment:talairach.jpg

Scroll through the slices and switch the views to get a good look at the transform. You will see some minor distortions, but you do not want to see any major rotations, translations, twisting or other means to skew the talairach from the orientation that your volume is in. Likewise, when you are looking at a coronal view of your volume you also want to be looking at a coronal view of the talairach. When you are done looking at the talairach you can turn it off by going to File -> Transforms -> Unload Transform for Main Volume.

Intensity Normalization

You want to be sure that the scan intensity is uniform. Scroll through the brainmask volume and make sure that you don't see any very bright or very dark spots. If you click on any voxel that is in the wm it should be normalized to an intensity of (or very close to) 110. The voxel intensity is shown in the Tkmedit Toolbox.

Skull Strip

You want to be sure that the skull strip step has succesfully removed all of the skull, and not taken away any of the cortex, cerebellum, or pons. You do want the cerebellum to be included in the brainmask volume. You

White Matter Volume

Final Surfaces

Subcortical Segmentation