top | Longitudinal Tutorial

Making FinalSurf edits

Below is a picture of how the longitudinal results for MR2 looked originally: see

tkmedit OAS2_0002_MR2.long.OAS2_0002 brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt


And here it is zoomed in:

Similarly, view the original longitudinal file for MR1 as follows:

tkmedit OAS2_0002_MR1.long.OAS2_0002 brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

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

For MR2, you would do:

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

For MR1, you would do:

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

In the 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 for MR2:

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 112 166 89 :

Zoomed in, we have:

For MR1, look at the results of re-running here:

tkmedit OAS2_0002_MR1.long.OAS2_0002_fixed brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt