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tkmedit pial_edits_before brainmask.mgz \
  
-aux T1.mgz -surfs
tkmedit pial_edits_before brainmask.mgz -aux T1.mgz -surfs
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tkmedit wm1_edits_before brainmask.mgz \
 
-aux T1.mgz -surfs
tkmedit wm1_edits_before brainmask.mgz -aux T1.mgz -surfs
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tkmedit wm1_edits_after brainmask.mgz \
  
-aux wm.mgz -surfs
tkmedit wm1_edits_after brainmask.mgz -aux wm.mgz -surfs
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tkmedit topo_defect_before brainmask.mgz \
 
-aux wm.mgz -surfs
tkmedit topo_defect_before brainmask.mgz -aux wm.mgz -surfs
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tkmedit topo_defect_after brainmask.mgz \
  
-aux wm.mgz -surfs
tkmedit topo_defect_after brainmask.mgz -aux wm.mgz -surfs
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tkmedit skullstrip1_before brainmask.mgz \
 
-aux T1.mgz -surfs
tkmedit skullstrip1_before brainmask.mgz -aux T1.mgz -surfs
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tkmedit cp_before brainmask.mgz \
 
-aux T1.mgz -surfs
tkmedit cp_before brainmask.mgz -aux T1.mgz -surfs
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tkmedit tal_before brainmask.mgz \
 
-aux T1.mgz -surfs
tkmedit tal_before brainmask.mgz -aux T1.mgz -surfs

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Troubleshooting your output

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.

  • If you are taking one of the formally organized courses, the data is already installed on the computer provided to you so please skip ahead to the Failure Modes section. 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.

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


tcsh
setenv SUBJECTS_DIR $TUTORIAL_DATA
cd $SUBJECTS_DIR

Failure Modes

Below, we ask you to look at several subjects with various errors that require manual intervention. Open each subject and try to identify the problem on your own. For each subject, there is a link to instructions on how to fix the problem. 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.

Edits to the brainmask volume

Open the subject, pial_edits_before.


tkmedit pial_edits_before brainmask.mgz -aux T1.mgz -surfs


The command above will open the brainmask.mgz volume, the T1.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.) Scroll through the slices of this subject to check the pial and white surfaces for accuracy, making sure they follow the actual gray/white boundaries and that they do not include anything that should not be included.

If you would like to see the inflated surfaces for each hemisphere of this subject, in a second and third terminal window, open the surfaces in tksurfer:


tksurfer pial_edits_before lh inflated 



tksurfer pial_edits_before rh inflated 


Once you have identified the problem (or have given up!), click here for detailed instructions on how you can fix it.

Edits to the wm volume

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


tkmedit wm1_edits_before brainmask.mgz  -aux T1.mgz -surfs


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

In your second and third 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 in the T1 volume to find the spot that does not match the actual gray/white boundary. 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.

Click here for detailed instructions on how you can fix it. You can also compare the original data to a corrected and rerun version, wm1_edits_after.

To view this corrected subject (which was corrected by following the detailed instructions provided to you):


tkmedit wm1_edits_after brainmask.mgz -aux wm.mgz -surfs


Correcting topological defects

Open the subject, topo_defect_before, in tkmedit.


tkmedit topo_defect_before brainmask.mgz  -aux wm.mgz -surfs


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

Take a look at this subject, inspecting the various outputs that were mentioned in the previous exercise and see if you can identify what is wrong.

Hint: It's a very small error in the posterior part of the brain.

Once you spot the error, click here for detailed instructions on how you can fix it. After you have fixed it, you can compare the original data to the a corrected and rerun version, topo_defect_after. To view this corrected subject:


tkmedit topo_defect_after brainmask.mgz -aux wm.mgz -surfs


Skull strip

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


tkmedit skullstrip1_before brainmask.mgz  -aux T1.mgz -surfs


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  -aux T1.mgz -surfs


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  -aux T1.mgz -surfs


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

In a second and third 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.

Editing the Aseg

We generally advise against editing the aseg.mgz unless absolutely necessary. Try using an xopts script first to change the intensity thresholds being used. Editing the aseg will add more variance to your data. Instructions on how to edit the aseg are here.

FsTutorial/TroubleshootingData_tktools (last edited 2013-11-01 14:24:23 by MaritzaEbling)