| Deletions are marked like this. | Additions are marked like this. |
| Line 34: | Line 34: |
| Now you can open the subject topo_defect_before, in tkmedit. | Now you can open the subject, topo_defect_before, in tkmedit. |
| Line 38: | Line 38: |
| lh.white -aux T1.mgz -aux-surface rh.white | lh.white -aux wm.mgz -aux-surface rh.white |
| Line 42: | Line 42: |
| This will open the brainmask.mgz volume, the T1.mgz loaded as aux, and the surfaces for both hemispheres. | This will open the brainmask.mgz volume, the wm.mgz loaded as aux, and the surfaces for both hemispheres. |
| Line 49: | Line 49: |
| Now, take a look at the next subject, subject2_before. | Now, take a look at the next subject, wm1_edits_before. |
| Line 52: | Line 52: |
| tkmedit subject2_before brainmask.mgz \ | tkmedit wm1_edits_before brainmask.mgz \ |
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.
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 subject2_before lh inflated & tksurfer subject2_before rh inflated &
This will open the inflated surfaces for both hemispheres in tksurfer.
You may need to open other volumes in order to see or fix the problem. Take a look through this subject and see if you can identify what is wrong.
If you are stuck and you need a hint you can click for some help.
When you think you've identified the problem, click here for detailed instructions on how you can fix it. You can also compare this to the finished version, subject2_after
Edits to the brainmask volume
Now, take a look at the next subject, subject3_before.
tkmedit subject3_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 subject3_before lh inflated & tksurfer subject3_before rh inflated &
This will open the inflated surfaces for both hemispheres in tksurfer.
You may need to open other volumes in order to see or fix the problem. Take a look through this subject and see if you can identify what is wrong.
If you are stuck and you need a hint you can click for some help.
When you think you've identified the problem, click here for detailed instructions on how you can fix it.
Skull strip
Now you can open the first subject, subject1_before, in tkmedit.
tkmedit subject1_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.
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 first subject, inspecting the various outputs that were mentioned in the previous exercise and see if you can indentify what is wrong.
If you are stuck and you need a hint you can click for some help.
When you think you've identified the problem, click here for detailed instructions on how you can fix it. You can also compare this to the finished version, subject1_after.
Adding control points
Now, take a look at the next subject, subject4_before.
tkmedit subject4_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 subject4_before lh inflated & tksurfer subject4_before rh inflated &
This will open the inflated surfaces for both hemispheres in tksurfer.
You may need to open other volumes in order to see or fix the problem. Take a look through this subject and see if you can identify what is wrong.
If you are stuck and you need a hint you can click for some help.
When you think you've identified the problem, click here for detailed instructions on how you can fix it.
Talairach transformation
Now, take a look at the next subject, subject5_before.
tkmedit subject5_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 subject5_before lh inflated & tksurfer subject5_before rh inflated &
This will open the inflated surfaces for both hemispheres in tksurfer.
You may need to open other volumes in order to see or fix the problem. Take a look through this subject and see if you can identify what is wrong.
If you are stuck and you need a hint you can click for some help.
When you think you've identified the problem, click here for detailed instructions on how you can fix it.