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| Deletions are marked like this. | Additions are marked like this. |
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| = Index = | [[Include(Blank, "Recon-all", 4)]] * ["recon-all"] * Commands, in chronological order: * ["mri_convert"] * ["mri_motion_correct.fsl"] * ["mri_nu_correct.mni"] * ["talairach"] * ["mri_normalize"] * ["mri_watershed"] * ["mri_em_register"] * ["mri_ca_normalize"] * ["mri_ca_register"] * ["mri_remove_neck"] * ["mri_ca_label"] * ["mri_segstats"] * ["mri_mask"] * ["mri_segment"] * ["mri_edit_wm_with_aseg"] * ["mri_pretess"] * ["mri_fill"] * ["mri_tessellate"] * ["mris_smooth"] * ["mris_inflate"] * ["mris_sphere"] * ["mris_fix_topology"] * ["mris_make_surfaces"] * ["mris_surf2vol"] * ["mris_register"] * ["mrisp_paint"] * ["mris_ca_label"] * ["mris_anatomical_stats"] * ["mri_aparc2aseg"] |
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| [[Navigation(children)]] [[TableOfContents]] |
[[Include(Blank, "Volume", 4)]] [[Include(FreeSurferCommandsVolumeConversion, , 5)]] [[Include(FreeSurferCommandsMotionCorrection, , 5)]] [[Include(FreeSurferCommandsTalairach, ,5)]] [[Include(FreeSurferCommandsRegistration, ,5)]] [[Include(FreeSurferCommandsIntensityNormalization, ,5)]] [[Include(FreeSurferCommandsSkullStripping, ,5)]] [[Include(FreeSurferCommandsSegmentation, ,5)]] [[Include(FreeSurferCommandsVolumeMisc, ,5)]] |
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| [[Anchor(Volume)]] = Volume = [[Anchor(VolumeConversion)]] == VolumeConversion == ["mri_convert"] [[BR]] ["brik2bfloat"] [[BR]] ["minc_to_bshort"] [[BR]] ["mri_annotation2label"] [[BR]] ["mri_convert_mdh"] [[BR]] ["mri_cor2label"] [[BR]] ["mri_label2label"] [[BR]] ["mri_surf2surf"] [[BR]] ["mri_surf2vol"] [[BR]] ["mri_vol2roi"] [[BR]] ["mri_vol2surf"] [[BR]] ["mri_volcluster"] [[BR]] ["spm2bfloat"] [[BR]] [[Anchor(MotionCorrection)]] == MotionCorrection == ["mri_motion_correct"] [[BR]] [[Anchor(Talairach)]] == Talairach == ["talairach"] {{BR}} [[Anchor(Registration)]] == Registration == ["mri_ca_register"] [[BR]] ["mri_register"] [[BR]] ["mri_rigid_register"] [[BR]] ["mri_linear_register"] [[BR]] [[Anchor(IntensityNormalization)]] == IntensityNormalization == ["mri_normalize"] [[BR]] [[Anchor(SkullStripping)]] == SkullStripping == ["mri_watershed"] [[Anchor(Segmentation)]] == Segmentation == ["mri_segment"] [[BR]] [[Anchor(VolumeMisc)]] == VolumeMisc == ["mkxsubjreg"] [[BR]] ["mri_add_xform_to_header"] [[BR]] ["mri_average"] [[BR]] ["mri_ca_label"] [[BR]] ["mri_ca_normalize"] [[BR]] ["mri_ca_train"] [[BR]] ["mri_em_register"] [[BR]] ["mri_fill"] [[BR]] ["mri_gdfglm"] [[BR]] ["mri_head"] [[BR]] ["mri_info"] [[BR]] ["mri_label_volume"] [[BR]] ["mri_make_register"] [[BR]] ["mri_make_template"] [[BR]] ["mri_matrix_multiply"] [[BR]] ["mri_ms_fitparms"] [[BR]] ["mri_parse_sdcmdir"] [[BR]] ["mri_partial_ribbon"] [[BR]] ["mri_probedicom"] [[BR]] ["mri_probe_ima"] [[BR]] ["mri_relabel_hypointensities"] [[BR]] ["mri_seghead"] [[BR]] ["mri_strip_skull"] [[BR]] ["mri_surfcluster"] [[BR]] ["mri_tessellate"] [[BR]] ["mri_volsynth"] [[BR]] ["mri_wmfilter"] [[BR]] ["mri_watershed"] [[BR]] ["mri_xvolavg"] [[BR]] [[Anchor(Surface)]] = Surface = [[Anchor(Surface Generation)]] == SurfaceConversion == [[Anchor(Smoothing)]] == Smoothing == [[Anchor(Inflation)]] == Inflation == [[Anchor(TopologyFixing)]] == TopologyFixing == [[Anchor(InterSubjectMorphing)]] == InterSubjectMorphing == [[Anchor(Parcellation)]] == Parcellation == [[Anchor(Flattening)]] == Flattening == [[Anchor(SurfaceMisc)]] == SurfaceMisc == |
[[Include(Blank, "Surface", 4)]] [[Include(FreeSurferCommandsSurfaceGeneration, ,5)]] [[Include(FreeSurferCommandsSurfaceSmoothing, ,5)]] [[Include(FreeSurferCommandsSurfaceInflation, ,5)]] [[Include(FreeSurferCommandsTopologyFixing, ,5)]] [[Include(FreeSurferCommandsInterSubjectMorphing, ,5)]] [[Include(FreeSurferCommandsFinalSurfaceGeneration, ,5)]] [[Include(FreeSurferCommandsSurfaceParcellation, ,5)]] [[Include(FreeSurferCommandsFlattening, ,5)]] [[Include(FreeSurferCommandsSurfaceMisc, ,5)]] |
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| ["mris2rgb"] [[BR]] ["mris_anatomical_statsv"] [[BR]] ["mris_average_curvature"] [[BR]] ["mris_ca_label"] [[BR]] ["mris_ca_train"] [[BR]] ["mris_convert"] [[BR]] ["mris_curvature"] [[BR]] ["mris_euler_number"] [[BR]] ["mris_find_flat_regions"] [[BR]] ["mris_fix_topology"] [[BR]] ["mris_flatten"] [[BR]] ["mris_glm"] [[BR]] ["mris_inflate"] [[BR]] ["mris_make_average_surface"] [[BR]] ["mris_make_surfaces"] [[BR]] ["mris_make_template"] [[BR]] ["mris_register"] [[BR]] ["mris_smooth"] [[BR]] ["mris_sphere"] [[BR]] ["mris_spherical_average"] [[BR]] ["mris_thickness"] [[BR]] ["mris_twoclass"] [[BR]] ["mrisp_paint"] [[BR]] ["mri_synthesize"] [[BR]] ["nmovie"] [[BR]] ["optseq2"] [[BR]] ["paint"] [[BR]] ["stat_normalize"] [[BR]] ["vss-dump"] [[BR]] |
Include(Blank, "Recon-all", 4)
- ["recon-all"]
- Commands, in chronological order:
- ["mri_convert"]
- ["mri_motion_correct.fsl"]
- ["mri_nu_correct.mni"]
- ["talairach"]
- ["mri_normalize"]
- ["mri_watershed"]
- ["mri_em_register"]
- ["mri_ca_normalize"]
- ["mri_ca_register"]
- ["mri_remove_neck"]
- ["mri_ca_label"]
- ["mri_segstats"]
- ["mri_mask"]
- ["mri_segment"]
- ["mri_edit_wm_with_aseg"]
- ["mri_pretess"]
- ["mri_fill"]
- ["mri_tessellate"]
- ["mris_smooth"]
- ["mris_inflate"]
- ["mris_sphere"]
- ["mris_fix_topology"]
- ["mris_make_surfaces"]
- ["mris_surf2vol"]
- ["mris_register"]
- ["mrisp_paint"]
- ["mris_ca_label"]
- ["mris_anatomical_stats"]
- ["mri_aparc2aseg"]
Include(FreeSurferCommandsVolumeConversion, , 5) Include(FreeSurferCommandsMotionCorrection, , 5) Include(FreeSurferCommandsTalairach, ,5) Include(FreeSurferCommandsRegistration, ,5) Include(FreeSurferCommandsIntensityNormalization, ,5) Include(FreeSurferCommandsSkullStripping, ,5) Include(FreeSurferCommandsSegmentation, ,5) Include(FreeSurferCommandsVolumeMisc, ,5)
Include(FreeSurferCommandsSurfaceGeneration, ,5) Include(FreeSurferCommandsSurfaceSmoothing, ,5) Include(FreeSurferCommandsSurfaceInflation, ,5) Include(FreeSurferCommandsTopologyFixing, ,5) Include(FreeSurferCommandsInterSubjectMorphing, ,5) Include(FreeSurferCommandsFinalSurfaceGeneration, ,5) Include(FreeSurferCommandsSurfaceParcellation, ,5) Include(FreeSurferCommandsFlattening, ,5) Include(FreeSurferCommandsSurfaceMisc, ,5)