top | Longitudinal Tutorial

Making FinalSurf edits

Below is a picture of how the longitudinal results for MR2 looked originally. Create a copy of 'brain.finalsurfs.mgz' named 'brain.finalsurfs.manedit.mgz' with the following command:

cp OAS2_0002_MR2.long.OAS2_0002/mri/brain.finalsurfs.mgz OAS2_0002_MR2.long.OAS2_0002/mri/brain.finalsurfs.manedit.mgz

Open the volume with the following:

freeview -v OAS2_0002_MR2.long.OAS2_0002/mri/brain.finalsurfs.manedit.mgz \
            OAS2_0002_MR2.long.OAS2_0002/mri/brainmask.mgz \
            OAS2_0002_MR2.long.OAS2_0002/mri/aseg.mgz:colormap=lut:opacity=0.25 \
         -f OAS2_0002_MR2.long.OAS2_0002/surf/lh.pial:edgecolor=red \
            OAS2_0002_MR2.long.OAS2_0002/surf/rh.pial:edgecolor=red \
            OAS2_0002_MR2.long.OAS2_0002/surf/lh.white:edgecolor=blue \
            OAS2_0002_MR2.long.OAS2_0002/surf/rh.white:edgecolor=blue

Sample Slice 89 in brain.finalsurfs.manedit.mgz, coordinates: 124 138 89 (right hemi)
longmr2BEFORE.jpg longmr2BEFOREzoomed.jpg

Similarly, create your copy of 'brain.finalsurfs.mgz' with the following command:

cp OAS2_0002_MR1.long.OAS2_0002/mri/brain.finalsurfs.mgz OAS2_0002_MR1.long.OAS2_0002/mri/brain.finalsurfs.manedit.mgz

View the original longitudinal file for MR1 as follows:

freeview -v OAS2_0002_MR1.long.OAS2_0002/mri/brain.finalsurfs.manedit.mgz \
            OAS2_0002_MR1.long.OAS2_0002/mri/brainmask.mgz \
            OAS2_0002_MR1.long.OAS2_0002/mri/aseg.mgz:colormap=lut:opacity=0.25 \
         -f OAS2_0002_MR1.long.OAS2_0002/surf/lh.pial:edgecolor=red \
            OAS2_0002_MR1.long.OAS2_0002/surf/rh.pial:edgecolor=red \
            OAS2_0002_MR1.long.OAS2_0002/surf/lh.white:edgecolor=blue \
            OAS2_0002_MR1.long.OAS2_0002/surf/rh.white:edgecolor=blue

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:

freeview -v OAS2_0002_MR2.long.OAS2_0002_fixed/mri/brain.finalsurfs.mgz \
            OAS2_0002_MR2.long.OAS2_0002_fixed/mri/brainmask.mgz \
            OAS2_0002_MR2.long.OAS2_0002_fixed/mri/aseg.mgz:colormap=lut:opacity=0.25 \
         -f OAS2_0002_MR2.long.OAS2_0002_fixed/surf/lh.pial:edgecolor=red \
            OAS2_0002_MR2.long.OAS2_0002_fixed/surf/rh.pial:edgecolor=red \
            OAS2_0002_MR2.long.OAS2_0002_fixed/surf/lh.white:edgecolor=blue \
            OAS2_0002_MR2.long.OAS2_0002_fixed/surf/rh.white:edgecolor=blue

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 :
longmr2FIXED.jpg longmr2FIXEDzoomed.jpg

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

freeview -v OAS2_0002_MR1.long.OAS2_0002_fixed/mri/brain.finalsurfs.mgz \
            OAS2_0002_MR1.long.OAS2_0002_fixed/mri/brainmask.mgz \
            OAS2_0002_MR1.long.OAS2_0002_fixed/mri/aseg.mgz:colormap=lut:opacity=0.25 \
         -f OAS2_0002_MR1.long.OAS2_0002_fixed/surf/lh.pial:edgecolor=red \
            OAS2_0002_MR1.long.OAS2_0002_fixed/surf/rh.pial:edgecolor=red \
            OAS2_0002_MR1.long.OAS2_0002_fixed/surf/lh.white:edgecolor=blue \
            OAS2_0002_MR1.long.OAS2_0002_fixed/surf/rh.white:edgecolor=blue