Difference between revisions of "Cerebellum CNN"

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<meta name="title" content="ACAPULCO: Cerebellum Parcellation with Convolutional Neural Networks"/>
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<!-- <meta name="title" content="ACAPULCO: Cerebellum Parcellation with Convolutional Neural Networks"/> -->
 
{{h2|Cerebellum Parcellation with Convolutional Neural Networks}}
 
{{h2|Cerebellum Parcellation with Convolutional Neural Networks}}
 
{{TOCright}}
 
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{{iacl-pub| author=S. Han, A. Carass, Y. He, and J.L. Prince| title=Automatic Cerebellum Anatomical Parcellation using U-Net with Locally Constrained Optimization| jrnl=ni| number=218:116819| when=2020| doi=10.1016/j.neuroimage.2020.116819}}
 
{{iacl-pub| author=S. Han, A. Carass, Y. He, and J.L. Prince| title=Automatic Cerebellum Anatomical Parcellation using U-Net with Locally Constrained Optimization| jrnl=ni| number=218:116819| when=2020| doi=10.1016/j.neuroimage.2020.116819}}
  
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It can be downloaded as a {{iacl|~shuo/data/acapulco.tar.gz |Docker image}}. The download is 1.2GB. If you use it please cite the above paper.
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If you have any questions, please email Shuo Han at <code>shan50@jhu.edu</code>.
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{|align="center" style="width:75%; border:2px #e99095 solid; background:#ffffff; text-align:left;"
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|-
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| colspan="3" align="center" | '''ACAPULCO'''
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|-
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<!--
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| {{iacl|~shuo/data/acapulco_022.tar.gz|Docker image CPU}}
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| 1.8GB
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|-
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| {{iacl|~shuo/data/acapulco_022_gpu.tar.gz|Docker image GPU}}
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| 2.5GB
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|-
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-->
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| {{iacl|~shuo/data/acapulco_030.sif|Singularity image CPU}}
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| Feb 27  2022
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| 1.8GB
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|-
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| {{iacl|~shuo/data/acapulco_030_gpu.sif|Singularity image GPU}}
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| Feb 27  2022
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| 2.5GB
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|-
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|}
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If you use it please cite the above paper. If you have any questions, please email Shuo Han at <code>shan50 _AT_ jhu.edu</code>.
 +
 
  
 
{{h3|Instructions}}
 
{{h3|Instructions}}
  
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The instructions are at [https://gitlab.com/shuohan/keras-unet-cerebellum/-/blob/master/README.md instructions].
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The instructions are available [https://gitlab.com/shuohan/keras-unet-cerebellum/-/blob/master/README.md here].
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{{h3| Delineation protocols: region names and voxel values}}
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* Adult training data:
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"Background":            0,
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"Corpus Medullare":      12,
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"Left I-III":            33,
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"Right I-III":            36,
 +
"Left IV":                43,
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"Rigt IV":                46,
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"Left V":                53,
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"Right V":                56,
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"Vermis VI":              60,
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"Left VI":                63,
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"Right VI":              66,
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"Vermis VII":            70,
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"Left Crus I":            73,
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"Left Crus II":          74,
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"Left VIIB":              75,
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"Right Crus I":          76,
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"Right Crus II":          77,
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"Right VIIB":            78,
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"Vermis VIII":            80,
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"Left VIIIA":            83,
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"Left VIIIB":            84,
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"Right VIIIA":            86,
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"Right VIIIB":            87,
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"Vermis IX":              90,
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"Left IX":                93,
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"Right IX":              96,
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"Vermis X":              100,
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"Left X":                103,
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"Right X":              106
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{{h3|Cerebellum labels}}
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* Pediatric training data:
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    "12": "Corpus_Medullare",
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"Background":             0,
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    "33": "Left_Lobules_I-III",
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  "Right Lobules I-V":      3,
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    "36": "Right_Lobules_I-III",
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"Right Lobule VI":         4,
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    "43": "Left_Lobule_IV",
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"Right Crus I":           5,
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    "46": "Right_Lobule_IV",
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"Right Crus II/VIIB":     6,
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    "53": "Left_Lobule_V",
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"Right Lobule VIII":       7,
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    "56": "Right_Lobule_V",
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"Right Lobule IX":         8,
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    "63": "Left_Lobule_VI",
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"Right Lobule X":         9,
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    "60": "Vermis_VI",
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  "Left Lobules I-V":       10,
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    "66": "Right_Lobule_VI",
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  "Left Lobule VI":         11,
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    "73": "Left_Lobule_VIIAf",
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  "Left Crus I":           12,
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    "76": "Right_Lobule_VIIAf",
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  "Left Crus II/VIIB":     13,
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    "74": "Left_Lobule_VIIAt",
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  "Left Lobule VIII":       14,
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    "70": "Vermis_VII",
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  "Left Lobule IX":         15,
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    "77": "Right_Lobule_VIIAt",
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  "Left Lobule X":         16,
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    "75": "Left_Lobule_VIIB",
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  "Vermis I-V":             17,
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    "78": "Right_Lobule_VIIB",
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  "Vermis VI-VII":         18,
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    "83": "Left_Lobule_VIIIA",
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"Vermis VIII-X":         19,
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    "80": "Vermis_VIII",
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"Corpus Medullare":       20
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    "86": "Right_Lobule_VIIIA",
 
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    "84": "Left_Lobule_VIIIB",
 
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    "87": "Right_Lobule_VIIIB",
 
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    "93": "Left_Lobule_IX",
 
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    "90": "Vermis_IX",
 
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    "96": "Right_Lobule_IX",
 
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    "103": "Left_Lobule_X",
 
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    "100": "Vermis_X",
 
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    "106": "Right_Lobule_X"
 

Latest revision as of 18:19, 2 November 2022

Cerebellum Parcellation with Convolutional Neural Networks

Automatic cerebellum anatomical parcellation using U-Net with locally constrained optimization (ACAPULCO) is our current cerebellum parcellation method. The associated publication is:

  • S. Han, A. Carass, Y. He, and J.L. Prince, "Automatic Cerebellum Anatomical Parcellation using U-Net with Locally Constrained Optimization", NeuroImage, 218:116819, 2020. (doi)


ACAPULCO
Singularity image CPU Feb 27 2022 1.8GB
Singularity image GPU Feb 27 2022 2.5GB


If you use it please cite the above paper. If you have any questions, please email Shuo Han at shan50 _AT_ jhu.edu.


Instructions

The instructions are available here.

Delineation protocols: region names and voxel values

  • Adult training data:
"Background":             0,
"Corpus Medullare":       12, 
"Left I-III":             33, 
"Right I-III":            36, 
"Left IV":                43, 
"Rigt IV":                46, 
"Left V":                 53, 
"Right V":                56, 
"Vermis VI":              60, 
"Left VI":                63, 
"Right VI":               66, 
"Vermis VII":             70, 
"Left Crus I":            73, 
"Left Crus II":           74, 
"Left VIIB":              75, 
"Right Crus I":           76, 
"Right Crus II":          77, 
"Right VIIB":             78, 
"Vermis VIII":            80, 
"Left VIIIA":             83, 
"Left VIIIB":             84, 
"Right VIIIA":            86, 
"Right VIIIB":            87, 
"Vermis IX":              90, 
"Left IX":                93, 
"Right IX":               96, 
"Vermis X":              100,
"Left X":                103,
"Right X":               106


  • Pediatric training data:
"Background":              0,
"Right Lobules I-V":       3,
"Right Lobule VI":         4,
"Right Crus I":            5,
"Right Crus II/VIIB":      6,
"Right Lobule VIII":       7,
"Right Lobule IX":         8,
"Right Lobule X":          9,
"Left Lobules I-V":       10,
"Left Lobule VI":         11,
"Left Crus I":            12,
"Left Crus II/VIIB":      13,
"Left Lobule VIII":       14,
"Left Lobule IX":         15,
"Left Lobule X":          16,
"Vermis I-V":             17,
"Vermis VI-VII":          18,
"Vermis VIII-X":          19,
"Corpus Medullare":       20
Retrieved from "https://iacl.ece.jhu.edu/index.php?title=Cerebellum_CNN&oldid=18241"