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Troubleshooting your output

• If you are taking one of the formally organized courses, the data is already installed on the computer provided to you. If not, then to follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. This set of exercises is not possible without the tutorial data set. Please set the environmental variable TUTORIAL_DATA to the location that you have downloaded the data to (here, it has been copied to $FREESURFER_HOME/subjects):

tcsh
setenv TUTORIAL_DATA $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs

• Notice the command to open tcsh. If you are already running the tcsh command shell, then the 'tcsh' command is not necessary.

This set of exercises will take you through a few examples of problem outputs, asking you to identify the problems and possible methods to fix the problems. Each example will have a before and after picture, as well as an explanation of how to fix the problems seen.

Below is a list of common things that require manual intervention. As you move through this exercise there will be links to pages instructing you how to fix these problems. While you are trying to identify the problems with the subjects listed below you may find it helpful to refer back to the previous exercise, or open your own instance of the subject good_output to compare these subjects to a good example.

<<==TableOfContents==>>

Correcting topological defects

First make sure you have your SUBJECTS_DIR set to the correct location:

tcsh
setenv SUBJECTS_DIR $TUTORIAL_DATA
cd $SUBJECTS_DIR

Now you can open the subject, topo_defect_before, in tkmedit.

tkmedit topo_defect_before brainmask.mgz \
  lh.white -aux wm.mgz -aux-surface rh.white

This will open the brainmask.mgz volume, the wm.mgz loaded as aux, and the surfaces for both hemispheres.

You can feel free to open other volumes in aux or to load in the aseg.mgz if you want or need to. Take a look at this subject, inspecting the various outputs that were mentioned in the previous exercise and see if you can indentify what is wrong.

Click here for detailed instructions on how you can fix it. You can also compare this to the finished version, topo_defect_after.

Edits to the wm volume

Now, take a look at the next subject, wm1_edits_before.

tkmedit wm1_edits_before brainmask.mgz \
  lh.white -aux T1.mgz -aux-surface rh.white

Again, this will bring up the brainmask.mgz volume, the T1.mgz volume, and the surfaces for both hemispheres.

In your second terminal window, if not already open, open the surfaces in tksurfer:

tksurfer wm1_edits_before lh inflated &
tksurfer wm1_edits_before rh inflated &

This will open the inflated surfaces for both hemispheres in tksurfer.

The trouble with this subject has occurred during the white matter segmentation step. Check the surfaces to find the spot that does not match the actual boundaries. If you load the wm.mgz volume as the aux volume you will see a hole in this area. If you are looking in tksurfer you will see a hole or dimple in the inflated surface. You can use the "save point" "goto point" commands to find this spot in the volume. You may need to open other volumes in order to see or fix the problem.

Click here for detailed instructions on how you can fix it. You can also compare this to the finished version, wm1_edits_after.

Edits to the brainmask volume

Now, take a look at the next subject, pial_edits_before.

tkmedit pial_edits_before brainmask.mgz \
  lh.white -aux T1.mgz -aux-surface rh.white

Again, this will bring up the brainmask.mgz volume, the T1.mgz volume, and the surfaces for both hemispheres.

In your second terminal window, if not already open, open the surfaces in tksurfer:

tksurfer pial_edits_before lh inflated &
tksurfer pial_edits_before rh inflated &

This will open the inflated surfaces for both hemispheres in tksurfer.

The trouble with this subject has occurred while making the final surfaces. Check the final surfaces (pial and white surfaces) to make sure that they follow the actual boundaries and that they do not include anything that should not be included.

You may need to open other volumes in order to see or fix the problem.

Click here for detailed instructions on how you can fix it.

Skull strip

Now, take a look at the next subject, skullstrip1_before, in tkmedit.

tkmedit skullstrip1_before brainmask.mgz \
  lh.white -aux T1.mgz -aux-surface rh.white

This will open the brainmask.mgz volume, the T1.mgz loaded as aux, and the surfaces for both hemispheres.

The trouble with this subject has occurred in the skull stripping step. Check the brainmask.mgz volume carefully, comparing it to the T1.mgz volume (loaded in aux) to make sure that the skull has been completely stripped away, leaving behind the complete cortex and the cerebellum.

You can feel free to open other volumes in aux or to load in the aseg.mgz if you want or need to.

Click here for detailed instructions on how you can fix it. You can also compare this to the finished version, skullstrip1_after.

Adding control points

Now, take a look at the next subject, cp_before.

tkmedit cp_before brainmask.mgz \
  lh.white -aux T1.mgz -aux-surface rh.white

Again, this will bring up the brainmask.mgz volume, the T1.mgz volume, and the surfaces for both hemispheres.

In your second terminal window, if not already open, open the surfaces in tksurfer:

tksurfer cp_before lh inflated &
tksurfer cp_before rh inflated &

This will open the inflated surfaces for both hemispheres in tksurfer.

The trouble with this subject has occured during the intensity normalization. Check the white surface and be sure it is including all of the white matter as it should. If you find an area that is not included as white matter be sure to check to see that the intensity is at (or very close to) 110.

You may need to open other volumes in order to see or fix the problem.

Click here for detailed instructions on how you can fix it.

Talairach transformation

Now, take a look at the next subject, tal_before.

tkmedit tal_before brainmask.mgz \
  lh.white -aux T1.mgz -aux-surface rh.white

Again, this will bring up the brainmask.mgz volume and the T1.mgz volume and the surfaces for both hemispheres.

In your second terminal window, if not already open, open the surfaces in tksurfer:

tksurfer tal_before lh inflated &
tksurfer tal_before rh inflated &

This will open the inflated surfaces for both hemispheres in tksurfer.

The trouble with this subject is a little tricky to figure out. The midline cutting planes are not actually on the midline, but the real root of this problem is in one of the very initial steps of recon-all. The talairach transform is bad and will need to be fixed.

You may need to open other volumes in order to see or fix the problem.

Click here for detailed instructions on how you can fix it.