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| recon-all -all -long OAS2_0002_MR1 OAS2_0002 | recon-all -long OAS2_0002_MR1 OAS2_0002 -all |
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| recon-all -all -long OAS2_0002_MR2 OAS2_0002 | recon-all -long OAS2_0002_MR2 OAS2_0002 -all |
Making FinalSurf edits
To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.
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 -long OAS2_0002_MR1 OAS2_0002 -all
mv OAS2_0002_MR2.long.OAS2_0002 OAS2_0002_MR2.long.OAS2_0002.old recon-all -long OAS2_0002_MR2 OAS2_0002 -all
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:
