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| *To follow this exercise exactly be sure you've downloaded the [https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data tutorial data set] before you begin. This set of exercises is not possible without the [https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data tutorial data set]. | [[FsTutorial|top]] | [[FsTutorial/OutputData|previous]] |
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| * 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 [[FsTutorial/Data|tutorial data set]] before you begin. This set of exercises is not possible without the [[FsTutorial/Data|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. |
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| This set of exercise 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. | 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. |
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| Below is a list of common things that require manual intervention. There is a link to a page describing how and when to use each of these edits. You can either read those now, or as needed while you go through this Troubleshooting exercise. | 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 [[FsTutorial/OutputData|previous exercise]], or open your own instance of the subject good_output to compare these subjects to a good example. |
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| *[wiki:Self:FsTutorial/SkullStripTutorial Skull strip] *[wiki:Self:FsTutorial/ControlPoints Adding control points] *[wiki:Self:FsTutorial/FixingGeomInaccuracies Edits to the wm volume] *[wiki:Self:FsTutorial/PialEdits Edits to the brainmask volume] |
*[[FsTutorial/TopologicalDefect|Correcting topological defect]] *[[FsTutorial/WhiteMatterEdits|Edits to the wm volume]] *[[FsTutorial/PialEdits|Edits to the brainmask volume]] *[[FsTutorial/SkullStripFix|Skull strip]] *[[FsTutorial/ControlPoints|Adding control points]] *[[FsTutorial/Talairach|Talairach transformation]] |
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| ---- | |
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| setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs | tcsh setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR |
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| ---- 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 |
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| 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 |
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| ---- | |
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| Open a second terminal window and open the surfaces in tksurfer: {{{ setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs tksurfer subject1_before lh inflated & tksurfer subject1_before rh inflated & }}} This will open the inflated surfaces for both hemisphere in tksurfer. |
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 [[FsTutorial/OutputData|previous exercise]] and see if you can indentify what is wrong. |
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| 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 [wiki:Self:FsTutorial/OutputData previous exercise] and see if you can indentify what is wrong. | If you are stuck and you need a [[FsTutorial/TroubleshootingHints|hint]] you can click for some help. |
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| If you are stuck and you need a [wiki:Self:FsTutorial/TroubleshootingHints hint] you can click for some help. When you think you've identified the problem, click [wiki:Self:FsTutorial/SkullStripFix here] for detailed instructions on how you can fix it. |
When you think you've identified the problem, click [[FsTutorial/SkullStripFix|here]] for detailed instructions on how you can fix it. You can also compare this to the finished version, subject1_after. |
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| ---- | |
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| tkmedit subject2_before brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white | tkmedit subject2_before brainmask.mgz \ lh.white -aux T1.mgz -aux-surface rh.white |
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| Again, this will bring up the brainmask.mgz volume and the T1.mgz volume and the surfaces for both hemispheres. | ---- Again, this will bring up the brainmask.mgz volume, the T1.mgz volume, and the surfaces for both hemispheres. |
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| ---- | |
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| setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs | |
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| ---- | |
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| If you are stuck and you need a [wiki:Self:FsTutorial/TroubleshootingHints hint] you can click for some help. | If you are stuck and you need a [[FsTutorial/TroubleshootingHints|hint]] you can click for some help. |
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| When you think you've identified the problem, click [wiki:Self:FsTutorial/WhiteMatterEdits here] for detailed instructions on how you can fix it. | When you think you've identified the problem, click [[FsTutorial/WhiteMatterEdits|here]] for detailed instructions on how you can fix it. You can also compare this to the finished version, subject2_after |
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| 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 [[FsTutorial/TroubleshootingHints|hint]] you can click for some help. When you think you've identified the problem, click [[FsTutorial/PialEdits|here]] for detailed instructions on how you can fix it. == Subject 4 == 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 [[FsTutorial/TroubleshootingHints|hint]] you can click for some help. When you think you've identified the problem, click [[FsTutorial/ControlPoints|here]] for detailed instructions on how you can fix it. == Subject 5 == 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 [[FsTutorial/TroubleshootingHints|hint]] you can click for some help. When you think you've identified the problem, click [[FsTutorial/Talairach|here]] for detailed instructions on how you can fix it. |
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.
Subject 1
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 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.
Subject 2
Now, take a look at the next subject, subject2_before.
tkmedit subject2_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
Subject 3
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.
Subject 4
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.
Subject 5
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.