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Making FinalSurf edits

Below is a picture of how the long for MR1 looked originally: Sample Slice 92 in brain.finalsurfs.mgz, coordinates:


And here it is zoomed in:

After edits to the cross and base have been done for each timepoint, the following commands should be run to re-create new long data sets:

mv OAS2_0002_MR1.long.OAS2_0002 OAS2_0002_MR1.long.OAS2_0002.old
recon-all -all -long OAS2_0002_MR1 OAS2_0002

mv OAS2_0002_MR2.long.OAS2_0002 OAS2_0002_MR2.long.OAS2_0002.old
recon-all -all -long OAS2_0002_MR2 OAS2_0002

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

tkmedit OAS2_0002_MR1.long.OAS2_0002_fixed brainmask.mgz -aux brain.finalsurfs.mgz -surfs
tkmedit OAS2_0002_MR2.long.OAS2_0002_fixed brainmask.mgz -aux brain.finalsurfs.mgz -surfs 

The following shows pictures of sample slice 92 from OAS2_0002_MR1.long.OAS2_0002_fixed in the brain.finalsurfs.mgz volume at coordinates:

Zoomed in, we have: