quickspecSL

Overview

This program makes a *.spec file after a set of intermediate surfaces
have been generated with SurfLayers.

It can also make a *.spec file that relates inflated surfaces to
anatomically-correct surfaces. An example of this is shown below in
the "Usage Example" section.

Options

-surf_A   SA   :inner (anatomically-correct) boundary surface dataset
                (e.g. smoothwm.gii)

-surf_B   SB   :outer (anatomically-correct) boundary surface dataset
                (e.g. pial.gii)

-surf_intermed_pref  SIP
               :prefix for (anatomically-correct) intermediate surfaces,
                typically output by SurfLayers
                (def: isurf)

-infl_surf_A  ISA
               :inner (inflated) boundary surface dataset
                (e.g. infl.smoothwm.gii)

-infl_surf_B  ISB
               :outer (inflated) boundary surface dataset
                (e.g. infl.pial.gii)

-infl_surf_intermed_pref  ISIP
               :prefix for (inflated) intermediate surfaces,
                typically output by SurfLayers
                (def: infl.isurf)

-both_lr       :specify an output spec for both hemispheres,
                if surfaces for both exist

-out_spec      :name for output *.spec file
                (def: newspec.spec)

Examples

1)

  quickspecSL                                  \
      -surf_A    lh.white.gii                  \
      -surf_B    lh.pial.gii                   \
      -surf_intermed_pref  lh.isurf


2)

  quickspecSL                                  \
      -both_lr                                 \
      -surf_A lh.white.gii                     \
      -surf_B lh.pial.gii


3) First, make inflated boundary surfaces before running SurfLayers
   on the both those and the original surfaces:

  SurfSmooth -i rh.smoothwm.gii -met NN_geom -Niter 240    \
      -o_gii -surf_out rh.inf.smoothwm_240 -match_size 9

  SurfSmooth -i rh.pial.gii -met NN_geom -Niter 240        \
      -o_gii -surf_out rh.inf.pial_240 -match_size 9

  quickspecSL                                              \
      -surf_A             rh.white.gii                     \
      -surf_B             rh.pial.gii                      \
      -surf_intermed_pref rh.isurf                         \
      -infl_surf_A        rh.inf.smoothwm_240.gii          \
      -infl_surf_B        rh.inf.pial_240.gii              \
      -infl_surf_intermed_pref  infl.rh.isurf

Notes

If you have any questions, please contact:

   S. Torrisi (salvatore.torrisi@ucsf.edu)
   D. Glen    (glend@mail.nih.gov)

for more info.