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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].  *To follow this exercise exactly be sure you've downloaded the [wiki:Self:FsTutorial/Data tutorial data set] before you begin. This set of exercises is not possible without the [wiki:Self:FsTutorial/Data tutorial data set].
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[wiki:FsTutorial top] | [wiki:FsTutorial/OutputData previous]

Troubleshooting your output

  • To follow this exercise exactly be sure you've downloaded the [wiki:FsTutorial/Data tutorial data set] before you begin. This set of exercises is not possible without the [wiki:FsTutorial/Data tutorial data set].

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 [wiki:FsTutorial/OutputData previous exercise], or open your own instance of the subject good_output to compare these subjects to a good example.

  • Skull strip
  • Edits to the wm volume
  • Edits to the brainmask volume
  • Adding control points
  • Talairach transformation

Subject 1

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

setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs

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.

Open a second terminal window and open the surfaces in tksurfer. First, be sure that the SUBJECTS_DIR is set appropriately:

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 hemispheres 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 [wiki:FsTutorial/OutputData previous exercise] and see if you can indentify what is wrong.

If you are stuck and you need a [wiki:FsTutorial/TroubleshootingHints hint] you can click for some help.

When you think you've identified the problem, click [wiki:FsTutorial/SkullStripFix 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:

setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
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 [wiki:FsTutorial/TroubleshootingHints hint] you can click for some help.

When you think you've identified the problem, click [wiki:FsTutorial/WhiteMatterEdits 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:

setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
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 [wiki:FsTutorial/TroubleshootingHints hint] you can click for some help.

When you think you've identified the problem, click [wiki: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:

setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
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 [wiki:FsTutorial/TroubleshootingHints hint] you can click for some help.

When you think you've identified the problem, click [wiki: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:

setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
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 [wiki:FsTutorial/TroubleshootingHints hint] you can click for some help.

When you think you've identified the problem, click [wiki:FsTutorial/Talairach here] for detailed instructions on how you can fix it.

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