[[FsTutorial|top]] | [[FsTutorial/LongitudinalTutorial|Longitudinal Tutorial]]

== Making FinalSurf edits ==
 * To follow this exercise exactly be sure you've downloaded the [[FsTutorial/Data|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 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/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: 111 166 89 (right hemi) <<BR>> {{attachment:longmr2BEFORE.jpg}} {{attachment:longmr2BEFOREzoomed.jpg}} <<BR>>

For MR1, similarly, create your copy of 'brain.finalsurfs.manedit.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/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 as a backup copy). For MR2, you would do:
{{{#!wiki caution
'''Don't run these recon-all commands'''

It will take hours and has already been done for you.
}}}
{{{
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/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 : <<BR>> {{attachment:longmr2FIXED.jpg}} {{attachment:longmr2FIXEDzoomed.jpg}} <<BR>>

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/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
}}}