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, especially if you made edits to the cross sectionals or base of that specific subject. 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.

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 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 if still necessary 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.

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 cross and base.

The wm.mgz (and consequently the filled.mgz) are used to create the surfaces.

WM edits should first be done in individual cross runs, if necessary. They are later automatically mapped and used in the long runs by default, therefore it should not be necessary to edit the longitudinal runs. Note that, if the wm.mgz in the long already contains edits (either manually or due to earlier transfer) it will not be updated.

In the long runs the surfaces are initialized with the surfaces from the base. Therefore, surfaces need to be accurate in the base, hence WM edits need to be done also there if necessary. Otherwise the longitudinal run might not recover from an incorrect initial surface placement even if it contains WM edits (e.g. transferred from cross).

Possible Shortcut: Optionally WM edits can be transferred from the base (instead of the cross runs) into specific longitudinal runs by specifying the -uselongbasewmedits flag to recon-all -long (in a 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).

Note, in either case (mapping edits from cross or transferring them from base) it is recommended to check if edits are accurately placed in long. They might move into neighboring voxels when taken from cross, due to interpolation of the mapping, or they might not be meaningful due to structural longitudinal change when taken from the base.

If the wm.mgz in the long directory contains edits (either transferred from cross or manual edits, which should be rarely necessary), no edits will be automatically transferred from cross or base. To allow transfer of new edits, just delete the wm.mgz in the long directory (possibly loosing any manual edits), merging is not possible.


1.5. aseg.mgz

ASEG edits can be done in cross, base and long.

Recommendation: 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.


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).


MartinReuter