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| [wiki:Self:FsTutorial top] | [wiki:Self:FsTutorial/MorphAndRecon previous] | = THIS PAGE HAS BEEN MOVED TO SHAREPOINT! = Please refer to this site/make edits here for the most updated information: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Volume-Processing-Stream.aspx ---- <<BR>> <<BR>> <<BR>> [[FsTutorial|top]] | [[FsTutorial/MorphAndRecon|previous]] |
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| attachment:volumepipelineSmall.gif | {{attachment:volumepipelineSmall.gif}} |
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| attachment:CN3Norm.jpg | {{attachment:CN3Norm.jpg}} |
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| attachment:CNorm.jpg | {{attachment:CNorm.jpg}} |
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| attachment:CTalairach.jpg | {{attachment:CTalairach.jpg}} |
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| attachment:CStripping.jpg | {{attachment:CStripping.jpg}} |
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| attachment:SCNormAndMask.jpg | {{attachment:SCNormAndMask.jpg}} |
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| attachment:SCSegment.jpg | {{attachment:SCSegment.jpg}} |
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| attachment:SCNormBrain.jpg | {{attachment:SCNormBrain.jpg}} |
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| attachment:SCSegmentWM.jpg | {{attachment:SCSegmentWM.jpg}} |
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| attachment:SCSegmentEditWM.jpg | {{attachment:SCSegmentEditWM.jpg}} |
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| attachment:SCfilling.jpg | {{attachment:SCfilling.jpg}} |
THIS PAGE HAS BEEN MOVED TO SHAREPOINT!
Please refer to this site/make edits here for the most updated information: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Volume-Processing-Stream.aspx
Image before and after comparisons (volume processing pipeline)
1.0 N3 intensity normalization: nu_correct_subject <subject name>
2.0 Cortical intensity normalization: mri_normalize orig T1
3.0 Cortical Talairach: talairach <subject name>
4.0 Cortical skull stripping: mri_watershed T1 brain
5.0 Subcortical intensity normalization: mri_ca_normalize -mask brain nu $GCA transforms/talairach.lta norm
6.0 Subcortical segmentation: mri_ca_label norm transforms/talairach.m3d $GCA aseg
7.0 Subcortical brain intensity normalization: mri_normalize norm brain
8.0 Subcortical white matter segmentation: mri_segment brain wm
9.0 Auto segmentation Editing: mri_edit_wm_with_aseg wm aseg wm
10.0 Filling: mri_fill wm filled
