-
Notifications
You must be signed in to change notification settings - Fork 12
Expand file tree
/
Copy pathreferences.bib
More file actions
554 lines (495 loc) · 19 KB
/
references.bib
File metadata and controls
554 lines (495 loc) · 19 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
@misc{brainprep-source,
title = "brainprepdesk/brainprep: v1.0.0",
author = "Grigis, Antoine and Victor, Julie and Dorval, Loic and
Duchesnay, Edouard",
url = "https://github.com/brainprepdesk/brainprep",
year = 2025,
}
@article{avants2009ants,
title = "The {ANTsX} ecosystem for quantitative biological and medical
imaging",
author = "Tustison, Nicholas J and Cook, Philip A and Holbrook, Andrew J
and Johnson, Hans J and Muschelli, John and Devenyi, Gabriel A
and Duda, Jeffrey T and Das, Sandhitsu R and Cullen, Nicholas C
and Gillen, Daniel L and Yassa, Michael A and Stone, James R and
Gee, James C and Avants, Brian B",
journal = "Sci. Rep.",
publisher = "Springer Science and Business Media LLC",
volume = 11,
number = 1,
pages = "9068",
month = apr,
year = 2021,
}
@article{jenkinson2012fsl,
title = "{FSL}",
author = "Jenkinson, Mark and Beckmann, Christian F and Behrens, Timothy E
J and Woolrich, Mark W and Smith, Stephen M",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 62,
number = 2,
pages = "782--790",
month = aug,
year = 2012,
}
@article{jenkinson2001flirt,
title = "A global optimisation method for robust affine registration of
brain images",
author = "Jenkinson, M and Smith, S",
journal = "Med. Image Anal.",
publisher = "Elsevier BV",
volume = 5,
number = 2,
pages = "143--156",
month = jun,
year = 2001,
}
@article{gaser2024cat12vbm,
title = "{CAT}: a computational anatomy toolbox for the analysis of
structural {MRI} data",
author = "Gaser, Christian and Dahnke, Robert and Thompson, Paul M and
Kurth, Florian and Luders, Eileen and {The Alzheimer's Disease
Neuroimaging Initiative}",
journal = "Gigascience",
publisher = "Oxford University Press (OUP)",
volume = 13,
month = jan,
year = 2024,
}
@article{desikan2006automated,
title = "An automated labeling system for subdividing the human cerebral
cortex on {MRI} scans into gyral based regions of interest",
author = "Desikan, Rahul S and S{\'e}gonne, Florent and Fischl, Bruce and
Quinn, Brian T and Dickerson, Bradford C and Blacker, Deborah
and Buckner, Randy L and Dale, Anders M and Maguire, R Paul and
Hyman, Bradley T and Albert, Marilyn S and Killiany, Ronald J",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 31,
number = 3,
pages = "968--980",
month = jul,
year = 2006,
}
@article{fischl2004automatically,
title = "Automatically parcellating the human cerebral cortex",
author = "Fischl, Bruce and van der Kouwe, Andr{\'e} and Destrieux,
Christophe and Halgren, Eric and S{\'e}gonne, Florent and Salat,
David H and Busa, Evelina and Seidman, Larry J and Goldstein,
Jill and Kennedy, David and Caviness, Verne and Makris, Nikos
and Rosen, Bruce and Dale, Anders M",
journal = "Cereb. Cortex",
publisher = "Oxford University Press (OUP)",
volume = 14,
number = 1,
pages = "11--22",
month = jan,
year = 2004,
}
@article{fischl1999cortical,
title = "Cortical surface-based analysis. {II}: Inflation, flattening,
and a surface-based coordinate system",
author = "Fischl, B and Sereno, M I and Dale, A M",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 9,
number = 2,
pages = "195--207",
month = feb,
year = 1999,
}
@article{greve2013surface,
title = "A surface-based analysis of language lateralization and cortical
asymmetry",
author = "Greve, Douglas N and Van der Haegen, Lise and Cai, Qing and
Stufflebeam, Steven and Sabuncu, Mert R and Fischl, Bruce and
Brysbaert, Marc",
journal = "J. Cogn. Neurosci.",
publisher = "MIT Press",
volume = 25,
number = 9,
pages = "1477--1492",
month = sep,
year = 2013,
}
@article{rosen2018,
title = "Quantitative assessment of structural image quality",
author = "Rosen, Adon F G and Roalf, David R and Ruparel, Kosha and Blake,
Jason and Seelaus, Kevin and Villa, Lakshmi P and Ciric, Rastko
and Cook, Philip A and Davatzikos, Christos and Elliott, Mark A
and Garcia de La Garza, Angel and Gennatas, Efstathios D and
Quarmley, Megan and Schmitt, J Eric and Shinohara, Russell T and
Tisdall, M Dylan and Craddock, R Cameron and Gur, Raquel E and
Gur, Ruben C and Satterthwaite, Theodore D",
journal = "Neuroimage",
volume = 169,
pages = "407--418",
month = apr,
year = 2018,
}
@article{almagro2018deface,
title = "Image processing and Quality Control for the first 10,000 brain
imaging datasets from {UK} Biobank",
author = "Alfaro-Almagro, Fidel and Jenkinson, Mark and Bangerter, Neal K
and Andersson, Jesper L R and Griffanti, Ludovica and Douaud,
Gwena{\"e}lle and Sotiropoulos, Stamatios N and Jbabdi, Saad and
Hernandez-Fernandez, Moises and Vallee, Emmanuel and Vidaurre,
Diego and Webster, Matthew and McCarthy, Paul and Rorden,
Christopher and Daducci, Alessandro and Alexander, Daniel C and
Zhang, Hui and Dragonu, Iulius and Matthews, Paul M and Miller,
Karla L and Smith, Stephen M",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 166,
pages = "400--424",
month = feb,
year = 2018,
}
@article{bischoff2007deface,
title = "A technique for the deidentification of structural brain {MR}
images",
author = "Bischoff-Grethe, Amanda and Ozyurt, I Burak and Busa, Evelina
and Quinn, Brian T and Fennema-Notestine, Christine and Clark,
Camellia P and Morris, Shaunna and Bondi, Mark W and Jernigan,
Terry L and Dale, Anders M and Brown, Gregory G and Fischl,
Bruce",
journal = "Hum. Brain Mapp.",
publisher = "Wiley",
volume = 28,
number = 9,
pages = "892--903",
month = sep,
year = 2007,
}
@misc{gulban2009deface,
title = "poldracklab/pydeface: v2.0.0",
author = "Gulban, O. F. and Nielson D. and Poldrack R.",
url = "https://zenodo.org/records/3524401",
year = 2009,
}
@article{cai2021prequal,
title = "{PreQual}: An automated pipeline for integrated preprocessing
and quality assurance of diffusion weighted {MRI} images",
author = "Cai, Leon Y and Yang, Qi and Hansen, Colin B and Nath, Vishwesh
and Ramadass, Karthik and Johnson, Graham W and Conrad, Benjamin
N and Boyd, Brian D and Begnoche, John P and Beason-Held, Lori L
and Shafer, Andrea T and Resnick, Susan M and Taylor, Warren D
and Price, Gavin R and Morgan, Victoria L and Rogers, Baxter P
and Schilling, Kurt G and Landman, Bennett A",
journal = "Magn. Reson. Med.",
publisher = "Wiley",
volume = 86,
number = 1,
pages = "456--470",
month = jul,
year = 2021
}
@article{tournier2019mrtrix,
title = "{MRtrix3}: A fast, flexible and open software framework for
medical image processing and visualisation",
author = "Tournier, J-Donald and Smith, Robert and Raffelt, David and
Tabbara, Rami and Dhollander, Thijs and Pietsch, Maximilian and
Christiaens, Daan and Jeurissen, Ben and Yeh, Chun-Hung and
Connelly, Alan",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 202,
number = 116137,
pages = "116137",
month = nov,
year = 2019,
}
@article{tustison2014ants,
title = "Large-scale evaluation of {ANTs} and {FreeSurfer} cortical
thickness measurements",
author = "Tustison, Nicholas J and Cook, Philip A and Klein, Arno and
Song, Gang and Das, Sandhitsu R and Duda, Jeffrey T and Kandel,
Benjamin M and van Strien, Niels and Stone, James R and Gee,
James C and Avants, Brian B",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 99,
pages = "166--179",
month = oct,
year = 2014,
}
@article{cordero2019mppca,
title = "Complex diffusion-weighted image estimation via matrix recovery
under general noise models",
author = "Cordero-Grande, Lucilio and Christiaens, Daan and Hutter, Jana
and Price, Anthony N and Hajnal, Jo V",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 200,
pages = "391--404",
month = oct,
year = 2019,
}
@article{andersson2016eddy,
title = "Incorporating outlier detection and replacement into a
non-parametric framework for movement and distortion correction
of diffusion {MR} images",
author = "Andersson, Jesper L R and Graham, Mark S and Zsoldos, Enik{\H o}
and Sotiropoulos, Stamatios N",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 141,
pages = "556--572",
month = nov,
year = 2016,
}
@article{veraart2013dti,
title = "Weighted linear least squares estimation of diffusion {MRI}
parameters: strengths, limitations, and pitfalls",
author = "Veraart, Jelle and Sijbers, Jan and Sunaert, Stefan and Leemans,
Alexander and Jeurissen, Ben",
journal = "Neuroimage",
volume = 81,
pages = "335--346",
month = nov,
year = 2013,
}
@article{lauzon2013qa,
title = "Simultaneous analysis and quality assurance for diffusion tensor
imaging",
author = "Lauzon, Carolyn B and Asman, Andrew J and Esparza, Michael L and
Burns, Scott S and Fan, Qiuyun and Gao, Yurui and Anderson, Adam
W and Davis, Nicole and Cutting, Laurie E and Landman, Bennett A",
journal = "PLoS One",
publisher = "Public Library of Science (PLoS)",
volume = 8,
number = 4,
pages = "e61737",
month = apr,
year = 2013,
}
@article{smith2002bet2,
title = "Fast robust automated brain extraction",
author = "Smith, Stephen M",
journal = "Hum. Brain Mapp.",
publisher = "Wiley",
volume = 17,
number = 3,
pages = "143--155",
month = nov,
year = 2002,
}
@article{jeurissen2014grad,
title = "Automated correction of improperly rotated diffusion gradient
orientations in diffusion weighted {MRI}",
author = "Jeurissen, Ben and Leemans, Alexander and Sijbers, Jan",
journal = "Med. Image Anal.",
publisher = "Elsevier BV",
volume = 18,
number = 7,
pages = "953--962",
month = oct,
year = 2014,
keywords = "Coordinate frame; Diffusion gradient reorientation;
Diffusion-weighted MRI; Fiber tractography; Stochastic
approximation",
language = "en"
}
@article{sanjari2025prequal,
title = "Microstructural alterations of the corpus callosum in affective
and non-affective early psychosis: A diffusion magnetic
resonance imaging study",
author = "Sanjari Moghaddam, Hossein and Aarabi, Mohammad Hadi and Kiani,
Iman and Cattarinussi, Giulia and Khodadadi, Shiva and Delavari,
Sahar and Sambataro, Fabio",
journal = "Schizophr. Res.",
publisher = "Elsevier BV",
volume = 284,
pages = "237--247",
month = sep,
year = 2025,
}
@article{smith2006tbss,
title = "Tract-based spatial statistics: voxelwise analysis of
multi-subject diffusion data",
author = "Smith, Stephen M and Jenkinson, Mark and Johansen-Berg, Heidi
and Rueckert, Daniel and Nichols, Thomas E and Mackay, Clare E
and Watkins, Kate E and Ciccarelli, Olga and Cader, M Zaheer and
Matthews, Paul M and Behrens, Timothy E J",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 31,
number = 4,
pages = "1487--1505",
month = jul,
year = 2006,
}
@article{esteban2017mriqc,
title = "MRIQC: Advancing the automatic prediction of image quality in
MRI from unseen sites",
author = "Esteban, Oscar and Birman, Daniel and Schaer, Marie and Koyejo,
Oluwasanmi O. and Poldrack, Russell A. and Gorgolewski,
Krzysztof J.",
journal = "PLOS ONE",
volume = 12,
number = 9,
pages = "e0184661",
year = 2017,
}
@article{fischl2012freesurfer,
title = "FreeSurfer",
author = "Fischl, Bruce",
journal = "NeuroImage",
volume = 62,
number = 2,
pages = "774--781",
year = 2012,
}
@article{dufumier2022openbhb,
title = "{OpenBHB}: A large-scale multi-site brain {MRI} data-set for age
prediction and debiasing",
author = "Dufumier, Benoit and Grigis, Antoine and Victor, Julie and
Ambroise, Corentin and Frouin, Vincent and Duchesnay, Edouard",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 263,
number = 119637,
pages = "119637",
month = nov,
year = 2022,
}
@article{schaer2008lgi,
title = "A surface-based approach to quantify local cortical gyrification",
author = "Schaer, Marie and Cuadra, Meritxell Bach and Tamarit, Lucas and
Lazeyras, Fran{\c c}ois and Eliez, Stephan and Thiran,
Jean-Philippe",
journal = "IEEE Trans. Med. Imaging",
publisher = "Institute of Electrical and Electronics Engineers (IEEE)",
volume = 27,
number = 2,
pages = "161--170",
month = feb,
year = 2008,
}
@article{hoopes2022brainmask,
title = "{SynthStrip}: skull-stripping for any brain image",
author = "Hoopes, Andrew and Mora, Jocelyn S and Dalca, Adrian V and
Fischl, Bruce and Hoffmann, Malte",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 260,
number = 119474,
pages = "119474",
month = oct,
year = 2022,
}
@article{greve2013xhemi,
title = "A surface-based analysis of language lateralization and cortical
asymmetry",
author = "Greve, Douglas N and Van der Haegen, Lise and Cai, Qing and
Stufflebeam, Steven and Sabuncu, Mert R and Fischl, Bruce and
Brysbaert, Marc",
journal = "J. Cogn. Neurosci.",
publisher = "MIT Press",
volume = 25,
number = 9,
pages = "1477--1492",
month = sep,
year = 2013,
}
@article{rosen2018euler,
title = "Quantitative assessment of structural image quality",
author = "Rosen, Adon F G and Roalf, David R and Ruparel, Kosha and Blake,
Jason and Seelaus, Kevin and Villa, Lakshmi P and Ciric, Rastko
and Cook, Philip A and Davatzikos, Christos and Elliott, Mark A
and Garcia de La Garza, Angel and Gennatas, Efstathios D and
Quarmley, Megan and Schmitt, J Eric and Shinohara, Russell T and
Tisdall, M Dylan and Craddock, R Cameron and Gur, Raquel E and
Gur, Ruben C and Satterthwaite, Theodore D",
journal = "Neuroimage",
volume = 169,
pages = "407--418",
month = apr,
year = 2018,
}
@article{esteban2019fmriprep,
title = "{fMRIPrep}: a robust preprocessing pipeline for functional {MRI}",
author = "Esteban, Oscar and Markiewicz, Christopher J and Blair, Ross W
and Moodie, Craig A and Isik, A Ilkay and Erramuzpe, Asier and
Kent, James D and Goncalves, Mathias and DuPre, Elizabeth and
Snyder, Madeleine and Oya, Hiroyuki and Ghosh, Satrajit S and
Wright, Jessey and Durnez, Joke and Poldrack, Russell A and
Gorgolewski, Krzysztof J",
journal = "Nat. Methods",
publisher = "Springer Science and Business Media LLC",
volume = 16,
number = 1,
pages = "111--116",
month = jan,
year = 2019,
}
@article{lesjak2016data,
title = "Validation of white-matter lesion change detection methods on a
novel publicly available {MRI} image database",
author = "Lesjak, {\v Z}iga and Pernu{\v s}, Franjo and Likar, Bo{\v
s}tjan and {\v S}piclin, {\v Z}iga",
journal = "Neuroinformatics",
publisher = "Springer Science and Business Media LLC",
volume = 14,
number = 4,
pages = "403--420",
month = oct,
year = 2016,
}
@article{landman2011data,
title = "Multi-parametric neuroimaging reproducibility: a {3-T} resource
study",
author = "Landman, Bennett A and Huang, Alan J and Gifford, Aliya and
Vikram, Deepti S and Lim, Issel Anne L and Farrell, Jonathan A D
and Bogovic, John A and Hua, Jun and Chen, Min and Jarso, Samson
and Smith, Seth A and Joel, Suresh and Mori, Susumu and Pekar,
James J and Barker, Peter B and Prince, Jerry L and van Zijl,
Peter C M",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 54,
number = 4,
pages = "2854--2866",
month = feb,
year = 2011,
}
@article{pinho2018ibc,
title = "Individual Brain Charting, a high-resolution {fMRI} dataset for
cognitive mapping",
author = "Pinho, Ana Lu{\'\i}sa and Amadon, Alexis and Ruest, Torsten and
Fabre, Murielle and Dohmatob, Elvis and Denghien, Isabelle and
Ginisty, Chantal and Becuwe-Desmidt, S{\'e}verine and Roger,
S{\'e}verine and Laurier, Laurence and Joly-Testault,
V{\'e}ronique and M{\'e}diouni-Cloarec, Ga{\"e}lle and
Doubl{\'e}, Christine and Martins, Bernadette and Pinel,
Philippe and Eger, Evelyn and Varoquaux, Ga{\"e}l and Pallier,
Christophe and Dehaene, Stanislas and Hertz-Pannier, Lucie and
Thirion, Bertrand",
journal = "Sci. Data",
volume = 5,
number = 1,
pages = "180105",
month = jun,
year = 2018,
}
@article{reuter2012freesurferlong,
title = "Within-subject template estimation for unbiased longitudinal
image analysis",
author = "Reuter, Martin and Schmansky, Nicholas J and Rosas, H Diana and
Fischl, Bruce",
journal = "Neuroimage",
publisher = "Elsevier BV",
volume = 61,
number = 4,
pages = "1402--1418",
month = jul,
year = 2012,
}
@article{fischer2012morphologist,
title = "Morphologist 2012: the new morphological pipeline of BrainVISA",
author = "Fischer, C. and Operto, Grégory and Laguitton, S. and
Perrot, Matthieu and Denghien, I. and Rivière, D.",
year = 2012,
journal = "Proceedings of the 18th HBM Scientific Meeting",
}