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.


1.1. control points

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

Default: 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 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.


1.2. talairach.xfm

Default: 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 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.

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.

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.

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.


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. If they are accurate in base, they should be accurate in long.


1.7. seed points, fill and cut

Seed points for cut/fill can be specified in cross, base and long.

So far they are not transfered.


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.


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