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== Image before and after comparisons (volume processing pipeline) ==

{{attachment:volumepipelineSmall.gif}}

=== 1.0 N3 intensity normalization: nu_correct_subject <subject name> ===

{{attachment:CN3Norm.jpg}}

=== 2.0 Cortical intensity normalization: mri_normalize orig T1 ===

{{attachment:CNorm.jpg}}

=== 3.0 Cortical Talairach: talairach <subject name> ===

{{attachment:CTalairach.jpg}}

=== 4.0 Cortical skull stripping: mri_watershed T1 brain ===

{{attachment:CStripping.jpg}}

=== 5.0 Subcortical intensity normalization: mri_ca_normalize -mask brain nu $GCA transforms/talairach.lta norm ===

{{attachment:SCNormAndMask.jpg}}

=== 6.0 Subcortical segmentation: mri_ca_label norm transforms/talairach.m3d $GCA aseg ===

{{attachment:SCSegment.jpg}}

=== 7.0 Subcortical brain intensity normalization: mri_normalize norm brain ===

{{attachment:SCNormBrain.jpg}}

=== 8.0 Subcortical white matter segmentation: mri_segment brain wm ===

{{attachment:SCSegmentWM.jpg}}

=== 9.0 Auto segmentation Editing: mri_edit_wm_with_aseg wm aseg wm ===

{{attachment:SCSegmentEditWM.jpg}}

=== 10.0 Filling: mri_fill wm filled ===

{{attachment:SCfilling.jpg}}