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.
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:
export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR
To copy: Highlight the command in the box above, right click and select copy (or use keyboard shortcut Ctrl+c), then use the middle button of your mouse to click inside the terminal window (this will paste the command). Press enter to run the command. These two commands set the SUBJECTS_DIR variable to the directory where the data is stored and then navigates into this directory. You can now skip ahead to the tutorial (below the gray line).
1.2. If You're Not at an Organized Course
If you are NOT taking one of the formally organized courses, then to follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. These are the commands that you need to run before getting started:
<source_freesurfer> export TUTORIAL_DATA=<path_to_your_tutorial_data> export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR
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.
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.
If you need a reminder of how to view the various outputs, you can refer back to the previous exercise. While troubleshooting, feel free to open other outputs for inspection.
2. Identifying errors
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Errors occur when recon-all finishes but your white or pial surfaces (or less frequently, your aseg) are inaccurate. When the surfaces are inaccurate, you have to manually change the information in a volume and regenerate the surface. It is not possible to directly edit the location of a surface.
3. Fixing errors
3.1. Edits to the brainmask volume
Open the subject, pial_edits_before.
freeview -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=red
NOTE: The backslash allows you to copy and paste multiple lines of code as one command. We use this throughout the tutorials to display the commands in a more easy-to-read manner, while still allowing you to copy and paste. Whenever you are typing in your own commands, instead of copying and pasting a command written out across multiple lines, a backslash is not necessary.
The command above will open the brainmask.mgz and T1.mgz volumes and the surfaces for both hemispheres. 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.
Once you have identified the problem (or have given up!), click here for detailed instructions on how you can fix it using Freeview.
You can also compare the original data to a corrected and rerun version, pial_edits_after. To view this corrected subject (which was corrected by following the detailed instructions provided to you):
freeview -v pial_edits_after/mri/T1.mgz \ pial_edits_after/mri/brainmask.mgz \ -f pial_edits_after/surf/lh.white:edgecolor=yellow \ pial_edits_after/surf/lh.pial:edgecolor=red \ pial_edits_after/surf/rh.white:edgecolor=yellow \ pial_edits_after/surf/rh.pial:edgecolor=red
3.2. Edits to the wm volume
Now, take a look at the next subject, wm1_edits_before.
freeview -v wm1_edits_before/mri/brainmask.mgz \ wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f wm1_edits_before/surf/lh.white:edgecolor=blue \ wm1_edits_before/surf/lh.pial:edgecolor=red \ wm1_edits_before/surf/rh.white:edgecolor=blue \ wm1_edits_before/surf/rh.pial:edgecolor=red \ wm1_edits_before/surf/rh.inflated:visible=0 \ wm1_edits_before/surf/lh.inflated:visible=0
Again, this will bring up the brainmask, the wm.mgz volume, the surfaces for both hemispheres, as well as the inflated surfaces.
The trouble with this subject has occurred during the white matter segmentation step. Check the surfaces in the brainmask volume to find the spot that does not match the actual gray/white boundary. In the wm.mgz volume you will see a hole in this area. If you are looking at the inflated surfaces in the 3D view, you will see a hole or dimple in the area in question.
Click here for detailed instructions on how you can fix it using Freeview.
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):
freeview -v wm1_edits_after/mri/T1.mgz \ wm1_edits_after/mri/brainmask.mgz \ -f wm1_edits_after/surf/lh.white:edgecolor=yellow \ wm1_edits_after/surf/lh.pial:edgecolor=red \ wm1_edits_after/surf/rh.white:edgecolor=yellow \ wm1_edits_after/surf/rh.pial:edgecolor=red
3.3. Correcting topological defects
Open the subject, topo_defect_before, in freeview.
freeview -v topo_defect_before/mri/brainmask.mgz \ topo_defect_before/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f topo_defect_before/surf/lh.white:edgecolor=yellow \ topo_defect_before/surf/lh.pial:edgecolor=red \ topo_defect_before/surf/rh.white:edgecolor=yellow \ topo_defect_before/surf/rh.pial:edgecolor=red
This will open the brainmask.mgz volume, the wm.mgz, and the surfaces for both hemispheres. Take a look at this subject 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 using Freeview.
After you have fixed it, you can compare the original data to the corrected and rerun version, topo_defect_after. To view this corrected subject:
freeview -v topo_defect_after/mri/brainmask.mgz \ topo_defect_after/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f topo_defect_after/surf/lh.white:edgecolor=yellow \ topo_defect_after/surf/lh.pial:edgecolor=red \ topo_defect_after/surf/rh.white:edgecolor=yellow \ topo_defect_after/surf/rh.pial:edgecolor=red
3.4. Skull strip
Now, take a look at the next subject, skullstrip1_before, in freeview.
freeview -v skullstrip1_before/mri/T1.mgz \ skullstrip1_before/mri/brainmask.mgz \ -f skullstrip1_before/surf/lh.white:edgecolor=yellow \ skullstrip1_before/surf/lh.pial:edgecolor=red \ skullstrip1_before/surf/rh.white:edgecolor=yellow \ skullstrip1_before/surf/rh.pial:edgecolor=red
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 to make sure that the skull has been completely stripped away, leaving behind the complete cortex and the cerebellum.
Click here for detailed instructions on how you can fix it using Freeview.
You can also compare this to the finished version, skullstrip1_after. To view this corrected subject:
freeview -v skullstrip1_after/mri/T1.mgz \ skullstrip1_after/mri/brainmask.mgz \ -f skullstrip1_after/surf/lh.white:edgecolor=yellow \ skullstrip1_after/surf/lh.pial:edgecolor=red \ skullstrip1_after/surf/rh.white:edgecolor=yellow \ skullstrip1_after/surf/rh.pial:edgecolor=red
3.5. Adding control points
Now, take a look at the next subject, cp_before.
freeview -v cp_before/mri/brainmask.mgz \ cp_before/mri/T1.mgz \ -f cp_before/surf/lh.white:edgecolor=blue \ cp_before/surf/lh.pial:edgecolor=red \ cp_before/surf/rh.white:edgecolor=blue \ cp_before/surf/rh.pial:edgecolor=red
The trouble with this subject has occurred 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 brainmask voxel intensity is at (or very close to) 110.
Click here for detailed instructions on how you can fix it using Freeview.
You can also compare the original data to a corrected and rerun version, cp_after. To view this corrected subject (which was corrected by following the detailed instructions provided to you):
freeview -v cp_after/mri/brainmask.mgz \ cp_after/mri/T1.mgz \ -f cp_after/surf/lh.white:edgecolor=blue \ cp_after/surf/lh.pial:edgecolor=red \ cp_after/surf/rh.white:edgecolor=blue \ cp_after/surf/rh.pial:edgecolor=red
3.6. Talairach transformation
Now, take a look at the next subject, tal_before.
freeview -v tal_before/mri/T1.mgz \ tal_before/mri/brainmask.mgz:reg=tal_before/mri/transforms/talairach.xfm
In a second terminal window, open the inflated surfaces in a new instance of freeview. (Note: Initially, only the right inflated hemisphere will be visible to prevent overlap)
freeview -f \ tal_before/surf/lh.inflated:visible=0 \ tal_before/surf/rh.inflated \ -viewport 3d
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.
Click here for detailed instructions on how you can fix it using Freeview.
After you have fixed it, you can compare the original data to the corrected and rerun version, tal_after. To view this corrected subject:
freeview -v tal_after/mri/T1.mgz \ tal_after/mri/brainmask.mgz:reg=tal_after/mri/transforms/talairach.xfm
3.7. Editing the Aseg
If you are at an organized course, this is NOT something you need to work on. This section is here to refer to if you run into issues at a later point.
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 using Freeview are here.
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4. Implementing fixes
4.1. Processing stream overview
4.2. Frequently used commands
5. Practice editing an entire subject
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