:orphan: .. _ahelp_quickspecSL: *********** quickspecSL *********** .. contents:: :local: | Overview ======== .. code-block:: none 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 ======= .. code-block:: none -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 ======== .. code-block:: none 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 ===== .. code-block:: none If you have any questions, please contact: S. Torrisi (torrisi@berkeley.edu) D. Glen (glend@mail.nih.gov) for more info.