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| Deletions are marked like this. | Additions are marked like this. |
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| Please read the description of edits see first: [[Edits]]. | Please read the description of edits first: [[Edits]]. |
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Generally, check and '''edit stuff as early in the stream as possible'''. That means first edit the cross sectional runs, rerun from that point to complete the cross sectional run, recreate the base (from scratch, i.e. remove or rename that directory). Check and edit the base, reprocess the base from that point, finally recreate the longitudinal from scratch (removing or renaming the directory if it existed) with the new base. Optimally there should be no editing necessary in the long runs, but it is recommended to check them. For exceptions and special treatment in specific cases see the detailed description below. Note, if you rerun a base or longitudinal from the start, make sure you '''delete or rename''' any existing directories to assert that edits are correctly copied over. Since the surfaces in the long are initialized with surfaces from the base, it is '''important to edit and fix surfaces in the base'''! Instead of doing everything the nice and clean way (editing as early as possible), you probably get away with just editing the base in most cases. When you re-run a base (template) or long run, even partially, you still '''need to pass -base or -long flags''' with the required arguments in addition to the desired parameters (e.g. -autorecon2 -autorecon3). Also after editing the base you should rerun the base with -autorecon2 AND -autorecon3 before running the longitudinals. Also note, you '''cannot rename''' any of the time points (cross or long) and rerun during this process. Renaming is only possible if you are recreating the base AND all longitudinal runs from scratch. Instead of renaming, when editing you might want to first '''create a backup copy''' of the existing directory for comparison and to have the option to go back to the earlier results later. |
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| Default: edit in cross. | ''Recommendation'': Edit in cross and base. |
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| If edits have been done to the cross, they are mapped and used in the long runs by default. Optionally, CP edits can be taken from the base by specifying the -uselongbasectrlvol. This can be helpful if longitudinal differences are expected to be very small (e.g. test-retest data). Then the CPs from the base are meaningful in all time points and can be transfered to all, instead of editing each TP individually. |
First CP edits should be done in the cross if necessary. They will influence the norm.mgz and therefore the base, so base and later the long runs need to be rerun (from scratch). If edits have been done to the cross, they are mapped and used in the long runs by default, so also editing the longitudinals should not be necessary! However it is necessary to also edit the base if the same problem still exists there. It should be asserted that the surfaces in the base are correct, because they are used to initialize surfaces in the longitudinal runs. |
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| In both cases (mapping CP from the cross, or transfering them from the base), it is recommended to check if they are accurately placed in the long. They might move into a neighboring voxel when taken from the cross, due to interpolation of the mapping, or they might not be meaningful due to longitudinal change when taken from the base. | ''Special cases with little longitudinal change'': Optionally, CP edits can transferred from the base (instead of the cross runs) into specific longitudinal runs by specifying the ''-uselongbasectrlvol'' in the -long run. This can be helpful if longitudinal structural differences are expected to be very small (e.g. test-retest data). Then the CPs from the base are meaningful in ''all'' affected time points and can be copied, instead of editing each TP individually. To check if an edit in the base is meaningful in several time points, you can open all these images on top of each other (e.g. using freeview), as they are in the same voxel space (since FS 5.1). In both cases (mapping CP from the cross, or transferring them from the base), it is recommended to check if all CPs are accurately placed in the long. They might move into a neighboring voxel when mapped from the cross, due to the resampling of the mapping, or they might not be meaningful due to longitudinal change when taken from the base. |
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| Default: Edit in cross and base. | ''Recommendation'': Edit in cross and base. |
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| The talairach.xfm is common for all long time points. It is taken from the base and needs to be checked and edited there. | A broken talairach.xfm can badly influence many downstream results. Therefore it is important to edit these problems if they occur, as early as in the cross sectionals. The talairach.xfm is common for all longitudinal runs. It is taken from the base and therefore also needs to be checked and edited there. |
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| Default: Edit the cross and if still necessary in the base. | ''Recommendation'': Edit the cross and base. |
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| The brainmask in the base is a logical OR of the brainmasks from the cross. Therefore, if the base is started after the cross have been edited and re-run, it will contain edits from the cross. The longitudinal runs all use the brainmask from the base, therefore the brainmask should be edited first in the cross, then in the base. | The brainmask in the base is a union (logical OR) of the brainmasks from the cross. Therefore, if the base is started after the cross have been edited and re-run, it will contain edits from the cross (delete the base if it already existed). The longitudinals all use the brainmask from the base, therefore the brainmask should be edited first in the cross, then in the base if it is still not correct there. |
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| In rare cases it might be problematic to edit a single brainmask for all time points (in the base) due to significant longitudinal change in the images. In that case the individual brainmask in the long runs can be edited. | ''Possible Shortcut'': It might be enough to only edit the base, the brainmask will be copied to the longitudinal runs and should fix things there. In rare occasions it might be problematic to use a single brainmask (from the base) for all time points due to significant longitudinal change in the images. In that case the individual brainmask in the long runs can be edited. Note that if the brainmask.mgz is available in the <tp>.long.<template>/mri directory it is assumed that it contains manual edits and will be kept untouched (i.e. edits from base will not be transferred). Therefore, you should either rerun the longitudinals from scratch or delete the brainmask.mgz to make sure your edits are correctly transferred. |
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| Default: Edit in cross. | ''Recommendation'': Edit in base. |
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| If edits have been done to the cross, they are mapped and used in the long runs by default. Optionally, WM edits can be taken from the base by specifying the -uselongbasewmedits. This can be helpful if longitudinal differences are expected to be very small (e.g. test-retest data). Then the edits from the base are meaningful in all time points and can be transfered to all, instead of editing each TP individually. |
The wm.mgz (and consequently the filled.mgz) are used to create the surfaces. Since the final surfaces of interests will be created in the long, and since those are initialized form sufaces in the base, it is essential to edit the base and fix any surface problems there. Otherwise a longitudinal run might not recover from the incorrect initial surface placement even if it contains WM edits. |
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| In both cases (mapping edits from the cross, or transfering them from the base), it is recommended to check if they are accurately placed in the long. They might move into a neighboring voxel when taken from the cross, due to interpolation of the mapping, or they might not be meaningful due to longitudinal change when taken from the base. | It is possible to edit WM in the cross sectionals to fix surfaces there, but these surfaces are ''currently'' not used later in the process. If cross is edited, WM edits will be automatically transferred to the longitudinals. Note that, if the wm.mgz in the long already contains edits (either manually or due to earlier transfer) it will not be updated (merging is not possible). WM edits only have a very limited influence on the surfaces in the longitudinal runs, therefore it should be sufficient to edit only the base. |
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| Default: Edit in cross. | ''Recommendation'': Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross. |
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| The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated into the long stream. | The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long. |
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| Default: Edit in base. | ''Recommendation'': Edit in base. |
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| The surfaces in long are initialized from the surfaces in base. If they are accurate in base, they should be accurate in long. (note: not tested) |
The surfaces in long are initialized from the surfaces in base. Edit the base to make sure surfaces are accurate in the base. |
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| Seed points for fill and cut can be edited in cross, base and long. | Seed points for cut/fill can be specified in cross, base and long. |
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| So far they are not transfered. | ''Recommendation'': Edit in base. |
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| (note: not tested) | The surfaces in long are initialized from the surfaces in base. Edit the base to make sure surfaces are accurate in the base. So far seed points are not transferred. |
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| Seed points for watershed can be specified in cross, base and long. | Seed points for watershed can be specified in cross only. |
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| So far they are not transferred. (note: not tested, future: ) |
In base and long the brainmasks are created from the cross sectional masks (union = logical OR). |
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| If a scan has a field-of-view (FOV) greater than 256, the -cw256 flag must be added to the recon-all in cross and long. | cw256 is specified only in cross. |
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| (note: not tested, future: check if -cw256 was passed in cross and automatically apply in long). | Both base and long will indirectly inherit this setting as they create their orig in the unbiased template space, cronstructed by registering the norm.mgz from the cross (which are FOV corrected). |
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| Expert options are not tested in base or long. | Expert options are currently not supported in base or long. Feel free to try if it works (and let us know). ---- MartinReuter |
1. Longitudinal Edits
This page describes how edits are done in the longitudinal FreeSurfer stream (-base and -long)
Please read the description of edits first: Edits.
Also make sure you understand the Longitudinal Stream: LongitudinalProcessing.
Generally, check and edit stuff as early in the stream as possible. That means first edit the cross sectional runs, rerun from that point to complete the cross sectional run, recreate the base (from scratch, i.e. remove or rename that directory). Check and edit the base, reprocess the base from that point, finally recreate the longitudinal from scratch (removing or renaming the directory if it existed) with the new base. Optimally there should be no editing necessary in the long runs, but it is recommended to check them. For exceptions and special treatment in specific cases see the detailed description below. Note, if you rerun a base or longitudinal from the start, make sure you delete or rename any existing directories to assert that edits are correctly copied over.
Since the surfaces in the long are initialized with surfaces from the base, it is important to edit and fix surfaces in the base! Instead of doing everything the nice and clean way (editing as early as possible), you probably get away with just editing the base in most cases.
When you re-run a base (template) or long run, even partially, you still need to pass -base or -long flags with the required arguments in addition to the desired parameters (e.g. -autorecon2 -autorecon3). Also after editing the base you should rerun the base with -autorecon2 AND -autorecon3 before running the longitudinals.
Also note, you cannot rename any of the time points (cross or long) and rerun during this process. Renaming is only possible if you are recreating the base AND all longitudinal runs from scratch. Instead of renaming, when editing you might want to first create a backup copy of the existing directory for comparison and to have the option to go back to the earlier results later.
1.1. control points
Control points edits can be done to the cross, the base and the long runs.
Recommendation: Edit in cross and base.
First CP edits should be done in the cross if necessary. They will influence the norm.mgz and therefore the base, so base and later the long runs need to be rerun (from scratch). If edits have been done to the cross, they are mapped and used in the long runs by default, so also editing the longitudinals should not be necessary! However it is necessary to also edit the base if the same problem still exists there. It should be asserted that the surfaces in the base are correct, because they are used to initialize surfaces in the longitudinal runs.
Special cases with little longitudinal change: Optionally, CP edits can transferred from the base (instead of the cross runs) into specific longitudinal runs by specifying the -uselongbasectrlvol in the -long run. This can be helpful if longitudinal structural differences are expected to be very small (e.g. test-retest data). Then the CPs from the base are meaningful in all affected time points and can be copied, instead of editing each TP individually. To check if an edit in the base is meaningful in several time points, you can open all these images on top of each other (e.g. using freeview), as they are in the same voxel space (since FS 5.1).
In both cases (mapping CP from the cross, or transferring them from the base), it is recommended to check if all CPs are accurately placed in the long. They might move into a neighboring voxel when mapped from the cross, due to the resampling of the mapping, or they might not be meaningful due to longitudinal change when taken from the base.
1.2. talairach.xfm
Recommendation: Edit in cross and base.
A broken talairach.xfm can badly influence many downstream results. Therefore it is important to edit these problems if they occur, as early as in the cross sectionals.
The talairach.xfm is common for all longitudinal runs. It is taken from the base and therefore also needs to be checked and edited there.
1.3. brainmask.mgz
The brainmask.mgz can be edited in the cross, base and long.
Recommendation: Edit the cross and base.
The brainmask in the base is a union (logical OR) of the brainmasks from the cross. Therefore, if the base is started after the cross have been edited and re-run, it will contain edits from the cross (delete the base if it already existed). The longitudinals all use the brainmask from the base, therefore the brainmask should be edited first in the cross, then in the base if it is still not correct there.
Possible Shortcut: It might be enough to only edit the base, the brainmask will be copied to the longitudinal runs and should fix things there.
In rare occasions it might be problematic to use a single brainmask (from the base) for all time points due to significant longitudinal change in the images. In that case the individual brainmask in the long runs can be edited.
Note that if the brainmask.mgz is available in the <tp>.long.<template>/mri directory it is assumed that it contains manual edits and will be kept untouched (i.e. edits from base will not be transferred). Therefore, you should either rerun the longitudinals from scratch or delete the brainmask.mgz to make sure your edits are correctly transferred.
1.4. wm.mgz
WM edits can be done in cross, base and long.
Recommendation: Edit in base.
The wm.mgz (and consequently the filled.mgz) are used to create the surfaces. Since the final surfaces of interests will be created in the long, and since those are initialized form sufaces in the base, it is essential to edit the base and fix any surface problems there. Otherwise a longitudinal run might not recover from the incorrect initial surface placement even if it contains WM edits.
It is possible to edit WM in the cross sectionals to fix surfaces there, but these surfaces are currently not used later in the process. If cross is edited, WM edits will be automatically transferred to the longitudinals. Note that, if the wm.mgz in the long already contains edits (either manually or due to earlier transfer) it will not be updated (merging is not possible). WM edits only have a very limited influence on the surfaces in the longitudinal runs, therefore it should be sufficient to edit only the base.
1.5. aseg.mgz
ASEG edits can be done in cross, base and long.
Recommendation: Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross.
The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long.
1.6. brain.finalsurfs.mgz
brain.finalsurfs.mgz edits can be done in cross and base.
Recommendation: Edit in base.
The surfaces in long are initialized from the surfaces in base. Edit the base to make sure surfaces are accurate in the base.
1.7. seed points, fill and cut
Seed points for cut/fill can be specified in cross, base and long.
Recommendation: Edit in base.
The surfaces in long are initialized from the surfaces in base. Edit the base to make sure surfaces are accurate in the base. So far seed points are not transferred.
1.8. seed point, watershed
Seed points for watershed can be specified in cross only.
In base and long the brainmasks are created from the cross sectional masks (union = logical OR).
1.9. cw256
cw256 is specified only in cross.
Both base and long will indirectly inherit this setting as they create their orig in the unbiased template space, cronstructed by registering the norm.mgz from the cross (which are FOV corrected).
1.10. expert options
Expert options are currently not supported in base or long. Feel free to try if it works (and let us know).