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Making FinalSurf edits

Below is a picture of how the long for MR2 looked originally: Sample Slice 89 in brain.finalsurfs.mgz, coordinates: 124 138 89 (right hemi)


And here it is zoomed in:

After edits to the cross and base have been done for timepoint 2, the following commands should be run to re-create new long data sets: (Start with renaming the existing long data to something like _orig)

mv OAS2_0002_MR2.long.OAS2_0002 OAS2_0002_MR2.long.OAS2_0002_orig
recon-all -all -long OAS2_0002_MR1 OAS2_0002

In these re-run the edits are automatically transferred from the cross-sectional. Also the fixed surfaces will be used from the base for initialization producing fixed results in the long run. The results of long re-run can be checked as follows:

tkmedit OAS2_0002_MR2.long.OAS2_0002_fixed brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt 

The following shows pictures of sample slice 89 from OAS2_0002_MR2.long.OAS2_0002_fixed in the brain.finalsurfs.mgz volume at coordinates:

Zoomed in, we have: