[[FsTutorial|top]] | [[FsTutorial/MorphAndRecon|previous]]

 *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.

== Visually check the cortical reconstruction output with tkmedit and tksurfer ==

For each step so far, look at the output generated for the subject 'bert'.  Each time you perform a cortical reconstruction, it is a good idea to visually examine the final surfaces generated after automatic topology fixing for errors or defects that may have been generated in the reconstruction steps.  First, set your subjects directory environment variable:

{{{
cd $TUTORIAL_DATA/buckner_data/tutorial_subjs
setenv SUBJECTS_DIR ${PWD}
}}}

'''Generating cutting planes and filling''' <<BR>>
This step takes the /bert/mri/wm.mgz segmented white matter volume as input, and outputs the bert/mri/filled.mgz volume.  To view this volume in tkmedit:

{{{
tkmedit bert filled.mgz
}}}

'''Tessellate''' <<BR>>
This step takes the /bert/mri/filled.mgz volume as input, and outputs the surfaces bert/surf/lh.orig and /bert/surf/rh.orig for the left and right hemispheres, respectively.  To view these surfaces in tksurfer:

{{{
tksurfer bert lh orig
tksurfer bert rh orig
}}}    

'''Smoothing and Inflation''' <<BR>>
The smoothing and inflation step takes the bert/surf/lh.orig and /bert/surf/rh.orig surfaces as input, and outputs the following surfaces in the bert/surf directory: lh.smoothwm, rh.smoothwm, lh.curv, rh.curv, lh.sulc, rh.sulc, lh.inflated, and rh.inflated.  To view the smoothed and inflated surfaces in tksurfer:

{{{
tksurfer bert lh smoothwm
tksurfer bert rh smoothwm
tksurfer bert lh inflated
tksurfer bert rh inflated
}}}

To view the curv files, load the lh inflated surface into tksurfer again.  Go to '''File -> Curvature -> Load Curvature...''', click '''Browse''', and select the file lh.curv.  You will see a red and green pattern overlaid on the inflated surface that represents the curvature of the white matter at that location.  Repeat with the right hemisphere inflated and curv files.

'''Generate final surfaces''' <<BR>>
The final surfaces are generated by taking the bert/surf/lh.orig and bert/surf/rh.orig surfaces as inputs, and outputs the following surfaces in the bert/surf directory: lh.white, rh.white, lh.pial, rh.pial, lh.thickness, rh.thickness. As mentioned previously, the white and pial surfaces are particularly important to check for defects before continuing through the surface processing pipeline. To view the surfaces in tksurfer:

{{{
tksurfer bert lh white
tksurfer bert rh white
tksurfer bert lh pial
tksurfer bert rh pial
}}}

'''Generate spherical surfaces''' <<BR>>
The spherical surface is generated by taking the bert/surf/lh.inflated and bert/surf/rh.inflated surfaces as inputs and outputting the surfaces bert/surf/lh.sphere and bert/surf/rh.sphere.  To view these files in tksurfer:

{{{
tksurfer bert lh sphere
tksurfer bert rh sphere
}}}

To make these spheres more interesting, view the curv files overlaid on the spherical surfaces.  Load the lh sphere surface into tksurfer again.  Go to '''File -> Curvature -> Load Curvature...''', click '''Browse''', and select the file lh.curv.  You will see a red and green pattern overlaid on the spherical surface that represents the curvature of the white matter at that location.  Repeat with the right hemisphere sphere and curv files.