Master Research Presentation<br />Automated Measurement of Brain Volumein Patients after aneurysmal Subarachnoid Hemorrhag...
Contents<br />Introduction<br />Methods<br />Data<br />Routine<br />Evaluation<br />Results<br />Discussion<br />Classific...
Introduction<br />What is aSAH?<br />After aSAH: brain damage<br /><ul><li> Introduction
 Methods
 Data
 Routine
 Evaluation
 Results
 Discussion
 Classification
 Strength and limitations
 Conclusion
 Questions</li></ul>source: thestrokefoundation.com<br />source: socialmediaseo.net<br />
Introduction<br />Annual incidence: 6 - 16 cases per 100,000<br />Fatality rate: 50 percent<br />50 percent of the survivo...
 Methods
 Data
 Routine
 Evaluation
 Results
 Discussion
 Classification
 Strength and limitations
 Conclusion
 Questions</li></li></ul><li>Introduction<br />Purpose: mapping brain volume<br />A new routine is needed<br />for accurat...
 Methods
 Data
 Routine
 Evaluation
 Results
 Discussion
 Classification
 Strength and limitations
 Conclusion
 Questions</li></li></ul><li>Methods - Data<br />Axial T1-weighted and T2-weighted images from a aSAH study 1. <br />10 tr...
 Methods
 Data
 Routine
 Evaluation
 Results
 Discussion
 Classification
 Strength and limitations
 Conclusion
 Questions</li></ul>1 Schaafsma JD et al. (2010) Intracranial aneurysms treated with coil placement: test characteristics ...
Methods - Routine<br /><ul><li> Introduction
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  • Brain damage examples: enlarged ventricles and infarcts
  • Represents only 7 percent of al strokes, average age: 50, more women
  • We know that psychological and neurological complaints are related to infarct size, but not all complaints are explained
  • BET did not work with lots of infarcts
  • Different distribution changes intensity
  • Classified samples are saved in probability maps
  • How good is the validaion set
  • Hierdoor SCS apart niet mee ondanks hoge score
  • Fractional vs. Probability instead of binary vs. probability
  • Can also be used for scans of patients after aSAH with same scan protocol.
  • Master Research Presentation

    1. 1. Master Research Presentation<br />Automated Measurement of Brain Volumein Patients after aneurysmal Subarachnoid Hemorrhage<br />Anne Kaspers<br /> source: socialmediaseo.net<br />
    2. 2. Contents<br />Introduction<br />Methods<br />Data<br />Routine<br />Evaluation<br />Results<br />Discussion<br />Classification issues<br />Strength and limitations<br />Conclusion<br />Questions<br />
    3. 3. Introduction<br />What is aSAH?<br />After aSAH: brain damage<br /><ul><li> Introduction
    4. 4. Methods
    5. 5. Data
    6. 6. Routine
    7. 7. Evaluation
    8. 8. Results
    9. 9. Discussion
    10. 10. Classification
    11. 11. Strength and limitations
    12. 12. Conclusion
    13. 13. Questions</li></ul>source: thestrokefoundation.com<br />source: socialmediaseo.net<br />
    14. 14. Introduction<br />Annual incidence: 6 - 16 cases per 100,000<br />Fatality rate: 50 percent<br />50 percent of the survivors suffer from neurological or cognitive deficits after a year<br /><ul><li> Introduction
    15. 15. Methods
    16. 16. Data
    17. 17. Routine
    18. 18. Evaluation
    19. 19. Results
    20. 20. Discussion
    21. 21. Classification
    22. 22. Strength and limitations
    23. 23. Conclusion
    24. 24. Questions</li></li></ul><li>Introduction<br />Purpose: mapping brain volume<br />A new routine is needed<br />for accurate brain volume measurement for 3 T MR images <br />for cerebral abnormalities<br />The routine is based on kNN using manually segmented MR image training data<br /><ul><li> Introduction
    25. 25. Methods
    26. 26. Data
    27. 27. Routine
    28. 28. Evaluation
    29. 29. Results
    30. 30. Discussion
    31. 31. Classification
    32. 32. Strength and limitations
    33. 33. Conclusion
    34. 34. Questions</li></li></ul><li>Methods - Data<br />Axial T1-weighted and T2-weighted images from a aSAH study 1. <br />10 training and 12 validation scans of patients after aSAH and control participants<br />Exclusion of patients with claustrophobia, neurosurgical clips, pacemaker, younger than 18 years<br /><ul><li> Introduction
    35. 35. Methods
    36. 36. Data
    37. 37. Routine
    38. 38. Evaluation
    39. 39. Results
    40. 40. Discussion
    41. 41. Classification
    42. 42. Strength and limitations
    43. 43. Conclusion
    44. 44. Questions</li></ul>1 Schaafsma JD et al. (2010) Intracranial aneurysms treated with coil placement: test characteristics of follow-up MR angiography--multicenter study. Radiology 1:209-218<br />
    45. 45. Methods - Routine<br /><ul><li> Introduction
    46. 46. Methods
    47. 47. Data
    48. 48. Routine
    49. 49. Evaluation
    50. 50. Results
    51. 51. Discussion
    52. 52. Classification
    53. 53. Strength and limitations
    54. 54. Conclusion
    55. 55. Questions</li></li></ul><li>Methods - Routine<br /><ul><li> Introduction
    56. 56. Methods
    57. 57. Data
    58. 58. Routine
    59. 59. Evaluation
    60. 60. Results
    61. 61. Discussion
    62. 62. Classification
    63. 63. Strength and limitations
    64. 64. Conclusion
    65. 65. Questions</li></ul>Input images<br />T1 and T2 weighted image<br />
    66. 66. Methods - Routine<br /><ul><li> Introduction
    67. 67. Methods
    68. 68. Data
    69. 69. Routine
    70. 70. Evaluation
    71. 71. Results
    72. 72. Discussion
    73. 73. Classification
    74. 74. Strength and limitations
    75. 75. Conclusion
    76. 76. Questions</li></ul>Registration<br />Registered T1 weighted image<br />and T2 weighted image<br />
    77. 77. Methods - Routine<br /><ul><li> Introduction
    78. 78. Methods
    79. 79. Data
    80. 80. Routine
    81. 81. Evaluation
    82. 82. Results
    83. 83. Discussion
    84. 84. Classification
    85. 85. Strength and limitations
    86. 86. Conclusion
    87. 87. Questions</li></ul>Mask Creation<br />Create mask to<br /> - include brain tissue<br /> - exclude skull and fatty tissue <br />
    88. 88. Methods - Routine<br /><ul><li> Introduction
    89. 89. Methods
    90. 90. Data
    91. 91. Routine
    92. 92. Evaluation
    93. 93. Results
    94. 94. Discussion
    95. 95. Classification
    96. 96. Strength and limitations
    97. 97. Conclusion
    98. 98. Questions</li></ul>Perform k-means<br />Image of 10 clusters <br />
    99. 99. Methods - Routine<br /><ul><li> Introduction
    100. 100. Methods
    101. 101. Data
    102. 102. Routine
    103. 103. Evaluation
    104. 104. Results
    105. 105. Discussion
    106. 106. Classification
    107. 107. Strength and limitations
    108. 108. Conclusion
    109. 109. Questions</li></ul>Create Mask<br />Selection of clusters and mask <br />
    110. 110. Methods - Routine<br /><ul><li> Introduction
    111. 111. Methods
    112. 112. Data
    113. 113. Routine
    114. 114. Evaluation
    115. 115. Results
    116. 116. Discussion
    117. 117. Classification
    118. 118. Strength and limitations
    119. 119. Conclusion
    120. 120. Questions</li></ul>Remove Cerebellum<br />Mask of the cerebrum on the T2 weigthed image<br />
    121. 121. Methods - Routine<br /><ul><li> Introduction
    122. 122. Methods
    123. 123. Data
    124. 124. Routine
    125. 125. Evaluation
    126. 126. Results
    127. 127. Discussion
    128. 128. Classification
    129. 129. Strength and limitations
    130. 130. Conclusion
    131. 131. Questions</li></ul>Extract Brain Images<br />Extracted Brain in the T1 and T2 weighted image<br />
    132. 132. Methods - Routine<br /><ul><li> Introduction
    133. 133. Methods
    134. 134. Data
    135. 135. Routine
    136. 136. Evaluation
    137. 137. Results
    138. 138. Discussion
    139. 139. Classification
    140. 140. Strength and limitations
    141. 141. Conclusion
    142. 142. Questions</li></ul>Shading Correction<br />T2 weighted image with and without shading<br />
    143. 143. Methods - Routine<br /><ul><li> Introduction
    144. 144. Methods
    145. 145. Data
    146. 146. Routine
    147. 147. Evaluation
    148. 148. Results
    149. 149. Discussion
    150. 150. Classification
    151. 151. Strength and limitations
    152. 152. Conclusion
    153. 153. Questions</li></ul>kNN Classification<br />
    154. 154. Methods - Routine<br />Training data <br />10 full segmentations<br />Subcortical structures, cortical grey matter, peripheral CSF and lateral ventricles<br />Only voxels without partial volume effect<br /><ul><li> Introduction
    155. 155. Methods
    156. 156. Data
    157. 157. Routine
    158. 158. Evaluation
    159. 159. Results
    160. 160. Discussion
    161. 161. Classification
    162. 162. Strength and limitations
    163. 163. Conclusion
    164. 164. Questions</li></ul>No partial volume effect<br />
    165. 165. Methods - Routine<br /><ul><li>A sample consist of a location, intensities and a label
    166. 166. Introduction
    167. 167. Methods
    168. 168. Data
    169. 169. Routine
    170. 170. Evaluation
    171. 171. Results
    172. 172. Discussion
    173. 173. Classification
    174. 174. Strength and limitations
    175. 175. Conclusion
    176. 176. Questions</li></ul>y<br />y<br />x<br />z<br />z<br />x<br />x<br />T1<br />T2<br />
    177. 177. Methods - Routine<br /><ul><li>What is feature space?
    178. 178. Introduction
    179. 179. Methods
    180. 180. Data
    181. 181. Routine
    182. 182. Evaluation
    183. 183. Results
    184. 184. Discussion
    185. 185. Classification
    186. 186. Strength and limitations
    187. 187. Conclusion
    188. 188. Questions</li></ul> Sample of Structure 1<br /> Sample of Structure 2<br />Intensity<br />Location<br />
    189. 189. Methods - Routine<br /><ul><li>How does k-Nearest Neigbor (kNN) work?
    190. 190. Introduction
    191. 191. Methods
    192. 192. Data
    193. 193. Routine
    194. 194. Evaluation
    195. 195. Results
    196. 196. Discussion
    197. 197. Classification
    198. 198. Strength and limitations
    199. 199. Conclusion
    200. 200. Questions</li></ul> Sample of Structure 1<br /> Sample of Structure 2<br />New Sample<br />Intensity<br />Location<br />
    201. 201. Methods - Routine<br /><ul><li>How does k-Nearest Neigbor (kNN) work?
    202. 202. Introduction
    203. 203. Methods
    204. 204. Data
    205. 205. Routine
    206. 206. Evaluation
    207. 207. Results
    208. 208. Discussion
    209. 209. Classification
    210. 210. Strength and limitations
    211. 211. Conclusion
    212. 212. Questions</li></ul> Sample of Structure 1<br /> Sample of Structure 2<br />New Sample<br />Intensity<br />Location<br />
    213. 213. Methods - Routine<br /><ul><li>How does k-Nearest Neigbor (kNN) work?
    214. 214. Introduction
    215. 215. Methods
    216. 216. Data
    217. 217. Routine
    218. 218. Evaluation
    219. 219. Results
    220. 220. Discussion
    221. 221. Classification
    222. 222. Strength and limitations
    223. 223. Conclusion
    224. 224. Questions</li></ul>k = 1<br /> Sample of Structure 1<br /> Sample of Structure 2<br />New Sample<br />Intensity<br />Location<br />
    225. 225. Methods - Routine<br /><ul><li>How does k-Nearest Neigbor (kNN) work?
    226. 226. Introduction
    227. 227. Methods
    228. 228. Data
    229. 229. Routine
    230. 230. Evaluation
    231. 231. Results
    232. 232. Discussion
    233. 233. Classification
    234. 234. Strength and limitations
    235. 235. Conclusion
    236. 236. Questions</li></ul>k = 1<br /> Sample of Structure 1<br /> Sample of Structure 2<br />New Sample<br />Intensity<br />Location<br />
    237. 237. Methods - Routine<br /><ul><li>How does k-Nearest Neigbor (kNN) work?
    238. 238. Introduction
    239. 239. Methods
    240. 240. Data
    241. 241. Routine
    242. 242. Evaluation
    243. 243. Results
    244. 244. Discussion
    245. 245. Classification
    246. 246. Strength and limitations
    247. 247. Conclusion
    248. 248. Questions</li></ul>k = 3<br /> Sample of Structure 1<br /> Sample of Structure 2<br />New Sample<br />Intensity<br />Location<br />
    249. 249. Methods - Routine<br /><ul><li>How does k-Nearest Neigbor (kNN) work?
    250. 250. Introduction
    251. 251. Methods
    252. 252. Data
    253. 253. Routine
    254. 254. Evaluation
    255. 255. Results
    256. 256. Discussion
    257. 257. Classification
    258. 258. Strength and limitations
    259. 259. Conclusion
    260. 260. Questions</li></ul>k = 3<br /> Sample of Structure 1<br /> Sample of Structure 2<br />New Sample<br />Intensity<br />Location<br />
    261. 261. Methods - Routine<br /><ul><li> Introduction
    262. 262. Methods
    263. 263. Data
    264. 264. Routine
    265. 265. Evaluation
    266. 266. Results
    267. 267. Discussion
    268. 268. Classification
    269. 269. Strength and limitations
    270. 270. Conclusion
    271. 271. Questions</li></ul>Remove Edge for subcortical structures and cortical grey matter <br />
    272. 272. Methods - Routine<br /><ul><li> Introduction
    273. 273. Methods
    274. 274. Data
    275. 275. Routine
    276. 276. Evaluation
    277. 277. Results
    278. 278. Discussion
    279. 279. Classification
    280. 280. Strength and limitations
    281. 281. Conclusion
    282. 282. Questions</li></ul>Move back CSF from lateral ventricles<br />Lateral ventricles before and after transfer CSF<br />
    283. 283. Methods - Routine<br /><ul><li> Introduction
    284. 284. Methods
    285. 285. Data
    286. 286. Routine
    287. 287. Evaluation
    288. 288. Results
    289. 289. Discussion
    290. 290. Classification
    291. 291. Strength and limitations
    292. 292. Conclusion
    293. 293. Questions</li></ul>Remove Infarcts<br />
    294. 294. Methods - Routine<br /><ul><li> Introduction
    295. 295. Methods
    296. 296. Data
    297. 297. Routine
    298. 298. Evaluation
    299. 299. Results
    300. 300. Discussion
    301. 301. Classification
    302. 302. Strength and limitations
    303. 303. Conclusion
    304. 304. Questions</li></ul>Final result<br />
    305. 305. Method - Evaluation<br />Validation by 2 observers<br />Half slices selected throughout the brain<br /><ul><li> Introduction
    306. 306. Methods
    307. 307. Data
    308. 308. Routine
    309. 309. Evaluation
    310. 310. Results
    311. 311. Discussion
    312. 312. Classification
    313. 313. Strength and limitations
    314. 314. Conclusion
    315. 315. Questions</li></ul>T2 weighted image, Subcortical structures, Cortical grey matter, Peripheral CSF and Lateral ventricles<br />
    316. 316. Method - Evaluation<br />Manual fraction combines information of multiple observers and multiple structures <br /><ul><li> Introduction
    317. 317. Methods
    318. 318. Data
    319. 319. Routine
    320. 320. Evaluation
    321. 321. Results
    322. 322. Discussion
    323. 323. Classification
    324. 324. Strength and limitations
    325. 325. Conclusion
    326. 326. Questions</li></ul>T2 weighted image, Subcortical structures, Cortical grey matter, Peripheral CSF and Lateral ventricles<br />
    327. 327. Method - Evaluation<br />Inter-observer agreement<br /><ul><li> Introduction
    328. 328. Methods
    329. 329. Data
    330. 330. Routine
    331. 331. Evaluation
    332. 332. Results
    333. 333. Discussion
    334. 334. Classification
    335. 335. Strength and limitations
    336. 336. Conclusion
    337. 337. Questions</li></ul>Observer segmentations<br />
    338. 338. Method - Evaluation<br />Routine validation<br /><ul><li> Introduction
    339. 339. Methods
    340. 340. Data
    341. 341. Routine
    342. 342. Evaluation
    343. 343. Results
    344. 344. Discussion
    345. 345. Classification
    346. 346. Strength and limitations
    347. 347. Conclusion
    348. 348. Questions</li></ul>Observer segmentations<br />Routine segmentations<br />
    349. 349. Method - Evaluation<br />Measuring agreement using: <br />Fractional Similarity Index (fSI)<br />Sensitivity and Specificity<br /><ul><li> Introduction
    350. 350. Methods
    351. 351. Data
    352. 352. Routine
    353. 353. Evaluation
    354. 354. Results
    355. 355. Discussion
    356. 356. Classification
    357. 357. Strength and limitations
    358. 358. Conclusion
    359. 359. Questions</li></li></ul><li>Results<br />Inter-observer agreement<br /><ul><li> Introduction
    360. 360. Methods
    361. 361. Data
    362. 362. Routine
    363. 363. Evaluation
    364. 364. Results
    365. 365. Discussion
    366. 366. Classification
    367. 367. Strength and limitations
    368. 368. Conclusion
    369. 369. Questions</li></li></ul><li>Results<br /><ul><li>Inter-observer agreement good for most structures (fSI > 0.80)
    370. 370. Introduction
    371. 371. Methods
    372. 372. Data
    373. 373. Routine
    374. 374. Evaluation
    375. 375. Results
    376. 376. Discussion
    377. 377. Classification
    378. 378. Strength and limitations
    379. 379. Conclusion
    380. 380. Questions</li></li></ul><li>Results<br />Routine validation results<br /><ul><li> Introduction
    381. 381. Methods
    382. 382. Data
    383. 383. Routine
    384. 384. Evaluation
    385. 385. Results
    386. 386. Discussion
    387. 387. Classification
    388. 388. Strength and limitations
    389. 389. Conclusion
    390. 390. Questions</li></li></ul><li>Results<br />Routine agreement good for subcortical structures, lateral ventricles, total brain and intracranial volume<br /><ul><li> Introduction
    391. 391. Methods
    392. 392. Data
    393. 393. Routine
    394. 394. Evaluation
    395. 395. Results
    396. 396. Discussion
    397. 397. Classification
    398. 398. Strength and limitations
    399. 399. Conclusion
    400. 400. Questions</li></li></ul><li>Results<br />Routine agreement good for subcortical structures, lateral ventricles, total brain and intracranial volume<br />Cortical grey matter, peripheral and total CSF fSI scores lower <br /><ul><li> Introduction
    401. 401. Methods
    402. 402. Data
    403. 403. Routine
    404. 404. Evaluation
    405. 405. Results
    406. 406. Discussion
    407. 407. Classification
    408. 408. Strength and limitations
    409. 409. Conclusion
    410. 410. Questions</li></li></ul><li>Discussion – Classification issues<br />Low scores of cortical grey matter because of :<br />Slice thickness larger than structure thickness<br />Unclear border<br />Perivascular spaces <br /><ul><li> Introduction
    411. 411. Methods
    412. 412. Data
    413. 413. Routine
    414. 414. Evaluation
    415. 415. Results
    416. 416. Discussion
    417. 417. Classification
    418. 418. Strength and limitations
    419. 419. Conclusion
    420. 420. Questions</li></li></ul><li>Discussion – Classification issues<br />Low scores of peripheral CSF because of<br />Slice thickness larger than structure thickness<br />Under-segmentation in training data<br /><ul><li> Introduction
    421. 421. Methods
    422. 422. Data
    423. 423. Routine
    424. 424. Evaluation
    425. 425. Results
    426. 426. Discussion
    427. 427. Classification
    428. 428. Strength and limitations
    429. 429. Conclusion
    430. 430. Questions</li></li></ul><li>Discussion – Strength and limitations<br />Strength:<br />fSI could better deal with probabilities<br />Limitation:<br />fractional observer values limited<br /><ul><li> Introduction
    431. 431. Methods
    432. 432. Data
    433. 433. Routine
    434. 434. Evaluation
    435. 435. Results
    436. 436. Discussion
    437. 437. Classification
    438. 438. Strength and limitations
    439. 439. Conclusion
    440. 440. Questions</li></li></ul><li>Conclusion<br />Automated routine is accurate for lateral ventricles, total brain and intracranial volume<br />It could be used for volume measurements in patients after aSAH<br /><ul><li> Introduction
    441. 441. Methods
    442. 442. Data
    443. 443. Routine
    444. 444. Evaluation
    445. 445. Results
    446. 446. Discussion
    447. 447. Classification
    448. 448. Strength and limitations
    449. 449. Conclusion
    450. 450. Questions</li></li></ul><li>Acknowledgments<br />ISI<br />Nelly Anbeek<br />Jeroen de Bresser<br />Hugo Kuijf<br />Max Viergever<br />Koen Vincken<br /><ul><li> Introduction
    451. 451. Methods
    452. 452. Data
    453. 453. Routine
    454. 454. Evaluation
    455. 455. Results
    456. 456. Discussion
    457. 457. Classification
    458. 458. Strength and limitations
    459. 459. Conclusion
    460. 460. Questions</li></ul>Neurology<br />Geert Jan Biessels<br />Gabriël Rinkel<br />Joanna Schaafsma<br />Others<br />Marja van Aken<br />Ekke Kaspers<br />Bart Waalewijn<br />
    461. 461. Questions<br /><ul><li> Introduction
    462. 462. Methods
    463. 463. Data
    464. 464. Routine
    465. 465. Evaluation
    466. 466. Results
    467. 467. Discussion
    468. 468. Classification
    469. 469. Strength and limitations
    470. 470. Conclusion
    471. 471. Questions</li>

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