|
Size: 3436
Comment: renamed from fswiki/TroubleshootingData
|
Size: 7918
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| *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]] |
| Line 4: | Line 4: |
| * 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. |
|
| Line 5: | Line 13: |
| 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. |
| Line 7: | Line 15: |
| 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. |
| Line 9: | Line 17: |
| *[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 defects]] *[[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]] |
| Line 14: | Line 25: |
| == Subject 1 == | == 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 |
| Line 16: | Line 40: |
| First make sure you have your SUBJECTS_DIR set to the correct location: | }}} ---- 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 [[FsTutorial/OutputData|previous exercise]] and see if you can indentify what is wrong. Click [[FsTutorial/TopologicalDefect|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. ---- |
| Line 18: | Line 52: |
| setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs | tkmedit wm1_edits_before brainmask.mgz \ lh.white -aux T1.mgz -aux-surface rh.white |
| Line 20: | Line 56: |
| ---- Again, this will bring up the brainmask.mgz volume, the T1.mgz volume, and the surfaces for both hemispheres. |
|
| Line 21: | Line 59: |
| Now you can open the first subject, subject1_before, in tkmedit. | In your second terminal window, if not already open, open the surfaces in tksurfer: ---- |
| Line 23: | Line 62: |
| tkmedit subject1_before brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white | tksurfer wm1_edits_before lh inflated & tksurfer wm1_edits_before rh inflated & |
| Line 25: | Line 65: |
| ---- 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 to find the spot that does not match the actual boundaries. 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. You may need to open other volumes in order to see or fix the problem. Click [[FsTutorial/WhiteMatterEdits|here]] for detailed instructions on how you can fix it. You can also compare this to the finished version, wm1_edits_after. == Edits to the brainmask volume == Now, take a look at the next subject, pial_edits_before. ---- {{{ tkmedit pial_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 pial_edits_before lh inflated & tksurfer pial_edits_before rh inflated & }}} ---- This will open the inflated surfaces for both hemispheres in tksurfer. The trouble with this subject has occurred while making the final surfaces. Check the final surfaces (pial and white surfaces) to make sure that they follow the actual boundaries and that they do not include anything that should not be included. You may need to open other volumes in order to see or fix the problem. Click [[FsTutorial/PialEdits|here]] for detailed instructions on how you can fix it. == Skull strip == Now, take a look at the next subject, skullstrip1_before, in tkmedit. ---- {{{ tkmedit skullstrip1_before brainmask.mgz \ lh.white -aux T1.mgz -aux-surface rh.white }}} ---- |
|
| Line 27: | Line 110: |
| Open a second terminal window and open the surfaces in tksurfer: | 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 [[FsTutorial/SkullStripFix|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. ---- |
| Line 29: | Line 120: |
| setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs tksurfer subject1_before lh inflated & tksurfer subject1_before rh inflated & |
tkmedit cp_before brainmask.mgz \ lh.white -aux T1.mgz -aux-surface rh.white |
| Line 33: | Line 124: |
| This will open the inflated surfaces for both hemisphere in tksurfer. | ---- Again, this will bring up the brainmask.mgz volume, the T1.mgz volume, and the surfaces for both hemispheres. |
| Line 35: | Line 127: |
| 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. | 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. |
| Line 37: | Line 136: |
| If you are stuck and you need a [wiki:Self:FsTutorial/TroubleshootingHints hint] you can click for some help. | 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. |
| Line 39: | Line 138: |
| When you think you've identified the problem, click [wiki:Self:FsTutorial/SkullStripFix here] for detailed instructions on how you can fix it. | You may need to open other volumes in order to see or fix the problem. |
| Line 41: | Line 140: |
| == Subject 2 == Now, take a look at the next subject, subject2_before. |
Click [[FsTutorial/ControlPoints|here]] for detailed instructions on how you can fix it. == Talairach transformation == Now, take a look at the next subject, tal_before. ---- |
| Line 44: | Line 146: |
| tkmedit subject2_before brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white | tkmedit tal_before brainmask.mgz \ lh.white -aux T1.mgz -aux-surface rh.white |
| Line 46: | Line 150: |
| ---- | |
| Line 49: | Line 154: |
| ---- | |
| Line 50: | Line 156: |
| setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs tksurfer subject2_before lh inflated & tksurfer subject2_before rh inflated & |
tksurfer tal_before lh inflated & tksurfer tal_before rh inflated & |
| Line 54: | Line 159: |
| ---- | |
| Line 56: | Line 162: |
| 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. | 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. |
| Line 58: | Line 164: |
| If you are stuck and you need a [wiki:Self:FsTutorial/TroubleshootingHints hint] you can click for some help. | You may need to open other volumes in order to see or fix the problem. |
| Line 60: | Line 166: |
| When you think you've identified the problem, click [wiki:Self:FsTutorial/WhiteMatterEdits here] for detailed instructions on how you can fix it. == Subject 3 == |
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.
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 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 to find the spot that does not match the actual boundaries. 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. 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. You can also compare this to the finished version, wm1_edits_after.
Edits to the brainmask volume
Now, take a look at the next subject, pial_edits_before.
tkmedit pial_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 pial_edits_before lh inflated & tksurfer pial_edits_before rh inflated &
This will open the inflated surfaces for both hemispheres in tksurfer.
The trouble with this subject has occurred while making the final surfaces. Check the final surfaces (pial and white surfaces) to make sure that they follow the actual boundaries and that they do not include anything that should not be included.
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.
Skull strip
Now, take a look at the next subject, skullstrip1_before, in tkmedit.
tkmedit skullstrip1_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.
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 \ 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 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 \ 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 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.