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, recreate the base (from scratch). Check and edit the base, reprocess the base from that point, finally recreate the longitudinal from scratch 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 description below.

When you re-run a base (template) or long run, even partially, you still need to pass -base or -long with the required arguments in addition to the desired parameter (e.g. -autorecon2 -autorecon3).

Also note, you cannot rename any of the time points (cross or long) and rerun during this process, unless you are recreating the base and long runs from scratch. However, you might want to create a backup copy of the old tp directory for comparison and to have the option to go back to the earlier results.


1.1. control points

Control points edits can be done to the cross, the base and the long runs.

Recommendation: edit in cross.

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 copied, instead of editing each TP individually.

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 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.

The talairach.xfm is common for all long time points. It is taken from the base and needs to be checked and edited there.


1.3. brainmask.mgz

The brainmask.mgz can be edited in the cross, base and long.

Default: 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.

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.


1.4. wm.mgz

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

Default: Edit in cross and base.

The wm.mgz (and consequently the filled.mgz) are used to create the surfaces. In the long runs the surfaces are initialized with the surfaces from the base. Therefore, they need to be accurate in the base, hence WM edits should be done there.

If WM edits were done in individual cross runs, they are mapped and used in the long runs by default. Optionally WM edits can be taken from the base by specifying the -uselongbasewmedits flag to recon-all. This can be helpful if longitudinal differences are expected to be very small (e.g. test-retest data). Then the edits from the base might be meaningful in all time points and can be transferred instead of edited in each TP individually.

Note, in either case (mapping edits from cross or transferring them from base) it is recommended to check if they 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 WM edits are done in long, no edits will be transferred from cross or base.


1.5. aseg.mgz

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

Default: 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 into the long stream.


1.6. brain.finalsurfs.mgz

brain.finalsurfs.mgz edits can be done in cross and base.

Default: 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.

Default: 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 crossectional masks (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