|
Size: 4178
Comment:
|
Size: 4635
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
| Please read the description of edits see first: [[Edits]]. | Please read the description of edits first: [[Edits]]. |
| Line 16: | Line 16: |
| Optionally, CP edits can be taken from the base by specifying the -uselongbasectrlvol. This can be helpful if longitudinal | Optionally, CP edits can be taken from the base by specifying the ''-uselongbasectrlvol''. This can be helpful if longitudinal |
| Line 18: | Line 18: |
| can be transfered to all, instead of editing each TP individually. | can be copied, instead of editing each TP individually. |
| Line 20: | Line 20: |
| 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. | 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. |
| Line 36: | Line 36: |
| 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 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 longitudinals all use the brainmask from the base, therefore the brainmask should be edited first in the cross, then in the base. |
| Line 45: | Line 45: |
| Default: Edit in cross. | Default: Edit in cross and base. |
| Line 47: | Line 47: |
| 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. 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. |
| Line 52: | Line 49: |
| 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. | 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. |
| Line 70: | Line 69: |
| 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. |
| Line 77: | Line 74: |
| Seed points for fill and cut can be edited in cross, base and long. | Seed points for cut/fill can be specified in cross and base. |
| Line 79: | Line 76: |
| So far they are not transfered. | Default: Edit in base. |
| Line 81: | Line 78: |
| (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. |
| Line 86: | Line 83: |
| Seed points for watershed can be specified in cross, base and long. | Seed points for watershed can be specified in cross only. |
| Line 88: | Line 85: |
| So far they are not transferred. | In base and long the brainmasks are created from the crossectional masks (logical OR). |
| Line 90: | Line 87: |
| (note: not tested, future: ) |
---- |
| Line 94: | Line 90: |
| 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. |
| Line 96: | Line 92: |
| (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). |
| Line 100: | Line 98: |
| 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.
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 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
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 longitudinals 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 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.
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 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.
1.8. 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).