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@article{AmthDeneRohl:2005,
author = {Amthauer, Holger and Deneke, Timm and Rohlfing, Torsten and
Ruf, Juri and B\"ohmig, M. and Gutberlet, M. and
Pl\"ockinger, U. and Felix, Roland and Lemke, Arne-J\"orn},
title = {Value of image fusion using single photon emission computed
tomography with integrated low dose computed tomography in
comparison with a retrospective voxel-based method in
neuroendocrine tumours},
journal = {European Radiology},
year = 2005,
volume = 15,
number = 7,
pages = {1456--1462},
month = {Jul.},
abstract = {The objective was the evaluation of single photon emission
computed tomography (SPECT) with integrated low dose
computed tomography (CT) in comparison with a retrospective
fusion of SPECT and high-resolution CT and a side-by-side
analysis for lesion localisation in patients with
neuroendocrine tumours. Twenty-seven patients were examined
by multidetector CT. Additionally, as part of somatostatin
receptor scintigraphy (SRS), an integrated SPECT-CT was
performed. SPECT and CT data were fused using software with
a registration algorithm based on normalised mutual
information. The reliability of the topographic assignment
of lesions in SPECT-CT, retrospective fusion and
side-by-side analysis was evaluated by two blinded
readers. Two patients were not enrolled in the final
analysis because of misregistrations in the retrospective
fusion. Eighty-seven foci were included in the analysis. For
the anatomical assignment of foci, SPECT-CT and
retrospective fusion revealed overall accuracies of 91 and
94\% (side-by-side analysis 86\%). The correct
identification of foci as lymph node manifestations (n=25)
was more accurate by retrospective fusion (88\%) than from
SPECT-CT images (76\%) or by side-by-side analysis
(60\%). Both modalities of image fusion appear to be well
suited for the localisation of SRS foci and are superior to
side-by-side analysis of non-fused images especially
concerning lymph node manifestations.},
keywords = {Image fusion; Single photon emission computed tomography;
Computed tomography; Neuroendocrine tumour; Somatostatine
receptor scintigraphy},
doi = {10.1007/s00330-004-2590-z},
pdf = {2005-amthauer-eurradiol-value_image_fusion_spect_ct_neuroendocrine.pdf},
pmid = 15627182,
url = {http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s00330-004-2590-z},
category = {journal},
copyright = {Copyright to this article is owned by Springer-Verlag. The
original publication is available at springerlink.com}
}
@article{ZahrFasaHsu:2009,
author = {Zahr, Natalie M. and Fasano Crawford, Elena L. and Hsu,
Oliver and Vinco, Shara and Mayer, Dirk and Rohlfing,
Torsten and Pfefferbaum, Adolf and Sullivan, Edith V.},
title = {In vivo glutamate decline associated with kainic-acid
induced status epilepticus},
journal = {Brain Research},
year = {2009},
optkey = {},
optvolume = { },
optnumber = { },
optpages = { },
optmonth = { },
optnote = {},
optannote = {},
abstract = {Neurophysiological, biochemical, and anatomical evidence
implicates glutamatergic mechanisms in epileptic
seizures. Until recently, however, longitudinal
characterization of in vivo glutamate dynamics was not
possible. Here, we present data using in vivo magnetic
resonance spectroscopy (MRS) optimized for the detection of
glutamate to identify changes that evolve following kainic
acid (KA)-induced status epilepticus. Wild-type male Wistar
rats underwent whole brain MR imaging and single voxel MRS
on a clinical 3T scanner equipped with a high-strength
insert gradient coil. Scanning took place before and then 3
days, 28 - 32 days, and 42 - 50 days after induction of
status epilepticus. Analyses compared 5 seizure (Sz), 5
no-seizure (NoSz; received KA but did not exhibit seizures),
and 6 control (Con) animals. This longitudinal study
demonstrated reduced glutamate levels in vivo in the dorsal
hippocampus 3 days and 1 month following status epilepticus
in Sz animals compared with Con animals. Additionally,
previous results were replicated: in the Sz group, computed
T2 was higher in the ventral hippocampus and limbic cortex 3
days after seizure activity compared with baseline but
resolved in both regions at the 1 month scan, suggesting a
transient edema. Three days following seizure activity,
N-acetylaspartate (NAA) declined and lactate increased in
the dorsal hippocampus of the Sz group compared with the Con
and NoSz group; both metabolites approached baseline levels
by the third scan. Taken together, these results support the
conclusion that seizure activity following KA infusion
causes loss of glutamatergic neurons.},
keywords = {Glutamate; Hippocampus; Cerebellum; Longitudinal; Rat;
Status epilepticus},
doi = {10.1016/j.brainres.2009.08.060},
pdf = {},
url = {http://www.sciencedirect.com/science/article/B6SYR-4X378FY-2/2/0335ff0a184d44cc4fa186ea6de5bd65},
category = {journal},
pmid = {19715683},
pmc = {}
}
@article{RohlZahrSull:2010,
author = {Rohlfing, Torsten and Zahr, Natalie M. and Sullivan, Edith
V. and Pfefferbaum, Adolf},
title = {The {SRI24} Multichannel Atlas of Normal Adult Human Brain
Structure},
journal = {Human Brain Mapping},
year = 2010,
volume = { },
number = { },
pages = {in press},
month = { },
abstract = { },
keywords = {brain atlas; multispectral magnetic resonance imaging;
diffusion tensor imaging; unbiased population registration;
spatial normalization; label propagation},
doi = {10.1002/hbm.20906},
pdf = { },
pmid = {},
pmc = {},
category = {journal}
}
@article{PfefRoseRohl:2009a,
author = {Pfefferbaum, Adolf and Rosenbloom, Margaret J. and Rohlfing,
Torsten and Kemper, Carol A. and Deresinski, Stanley and
Sullivan, Edith V.},
title = {Frontostriatal Fiber Bundle Compromise in {HIV} Infection
without Dementia},
journal = {AIDS},
year = {2009},
volume = 23,
number = 15,
pages = {1977--1985},
month = {Sep.},
abstract = {Background: Quantitative fiber tracking derived from
diffusion tensor imaging (DTI) was used to determine whether
white matter association, projection, or commissural tracts
are affected in nondemented individuals with HIV infection
and to identify the regional distribution of sparing and
impairment of fiber systems.
Methods: DTI measured fractional anisotropy and diffusivity,
quantified separately for longitudinal ([lambda]L)
diffusivity (index of axonal injury) and transverse
([lambda]T) diffusivity (index of myelin injury), in 11
association and projection white matter tracts and six
commissural tracts in 29 men and 13 women with HIV infection
and 88 healthy, age-matched controls (42 men and 46 women).
Results: The total group of HIV-infected individuals had
higher diffusivity (principally longitudinal) than controls
in the posterior sectors of the corpus callosum, internal
and external capsules, and superior cingulate bundles. High
longitudinal diffusivity, indicative of axonal compromise,
was especially prominent in posterior callosal sectors,
fornix, and superior cingulate bundle in HIV with
AIDS. Unmedicated patients had notably high transverse
diffusivity, indicative of myelin compromise, in the
occipital forceps, inferior cingulate bundle, and superior
longitudinal fasciculus. Pontocerebellar projection fibers
were resistant to HIV effects as were commissural fibers
coursing through premotor and sensorimotor callosal
sectors.
Conclusion: This quantitative survey of brain fiber tract
integrity indicates that even nondemented HIV patients can
have neuroradiological evidence for damage to association
and commissural tracts. These abnormalities were vulnerable
to exacerbation with AIDS and possibly mitigated by HAART.},
doi = {10.1097/QAD.0b013e32832e77fe},
keywords = {AIDS, brain, cognition, dementia, diffusion tensor imaging,
HAART, HIV, MRI, white matter},
url = {http://journals.lww.com/aidsonline/pages/articleviewer.aspx?year=2009&issue=09240&article=00006&type=abstract},
pdf = {2009-pfefferbaum-aids-frontostriatal_fiber_compromise_hiv.pdf},
pmid = {19730350},
pmc = {In process},
category = {journal}
}
@article{PfefAdalRohl:2009a,
author = {Pfefferbaum, Adolf and Adalsteinsson, Elfar and Rohlfing,
Torsten and Sullivan, Edith V.},
title = {{MRI} Estimates of Brain Iron Concentration in Normal Aging:
Comparison of Field-Dependent ({FDRI}) and Phase ({SWI})
Methods},
journal = {NeuroImage},
year = 2009,
volume = 47,
number = 2,
pages = {493--500},
month = {Aug.},
abstract = {Different brain structures accumulate iron at different
rates throughout the adult life span. Typically, striatal
and brain stem structures are higher in iron concentrations
in older than younger adults, whereas cortical white matter
and thalamus have lower concentrations in the elderly than
young adults. Brain iron can be measured in vivo with MRI by
estimating the relaxivity increase across magnetic field
strengths, which yields the Field-Dependent R2 Increase
(FDRI) metric. The influence of local iron deposition on
susceptibility, manifest as MR phase effects, forms the
basis for another approach for iron measurement,
Susceptibility-Weighted Imaging (SWI), for which imaging at
only one field strength is sufficient. Here, we compared the
ability of these two methods to detect and quantify brain
iron in 11 young (5 men, 6 women; 21 to 29 years) and 12
elderly (6 men, 6 women; 64 to 86 years) healthy
adults. FDRI was acquired at 1.5T and 3.0T, and SWI was
acquired at 1.5T. The results showed that both methods
detected high globus pallidus iron concentration regardless
of age and significantly greater iron in putamen with
advancing age. The SWI measures were more sensitive when the
phase signal intensities themselves were used to define
regions of interest, whereas FDRI measures were robust to
the method of region of interest selection. Further, FDRI
measures were more highly correlated than SWI iron estimates
with published postmortem values and were more sensitive
than SWI to iron concentration differences across basal
ganglia structures. Whereas FDRI requires more imaging time
than SWI, two field strengths, and across-study image
registration for iron concentration calculation, FDRI
appears more specific to age-dependent accumulation of
non-heme brain iron than SWI, which is affected by heme iron
and non-iron source effects on phase.},
doi = {10.1016/j.neuroimage.2009.05.006},
pdf = {2009-pfefferbaum-nimg-mri_brain_iron_fdri_swi_comparison.pdf},
pmid = 19442747,
pmc = { },
category = {journal}
}
@article{LuedProcRohl:2009,
author = {L\"u{}demann, Lutz and Prochnow, Daniel and Rohlfing,
Torsten and Franiel, Tobias and Warmuth, Carsten and
Taupitz, Matthias and Rehbein, Hagen and Beyersdorff, Dirk},
title = {Simultaneous Quantification of Perfusion and Permeability in
the Prostate Using Dynamic Contrast-Enhanced Magnetic
Resonance Imaging with an Inversion-Prepared Dual-Contrast
Sequence},
journal = {Annals of Biomedical Engineering},
year = 2009,
volume = 37,
number = 4,
pages = {749--762},
month = {Apr.},
abstract = {The aim of the present study was to quantify both perfusion
and extravasation in the prostate to discriminate tumor from
healthy tissue, which might be achieved by dynamic
contrast-enhanced magnetic resonance imaging (DCE-MRI) using
a nonspecific low-molecular-weight contrast medium (CM). To
determine extravasation as well as tissue perfusion an
inversion-prepared dual-contrast sequence employing a
parallel acquisition technique (PAT) was designed for
interleaved acquisition of T (1)-weighted images for
extravasation measurement and T2[Formula: see text]-weighted
images for determination of the highly concentrated bolus
with a sufficiently high temporal and spatial resolution at
an acceptable signal-to-noise ratio. Thirteen patients with
proven prostate cancer were examined with the sequence using
a combined body-array prostate coil. Before pharmacokinetic
evaluation the images were intensity-corrected and, if
required, motion-corrected. The pharmacokinetic model used
to calculate perfusion, permeability, blood volume,
interstitial volume, transit time, and vessel size index
included two compartments and a correction of delay and
dispersion of the arterial input function. The information
provided by the dual-contrast sequence allowed application
of a more elaborate model for evaluation and enabled
quantification of all parameters. Peripheral prostate tumors
were found to differ from peripheral healthy prostate tissue
in perfusion (1.38 mL/(min cm(3)) vs. 0.23 mL/(min cm(3)), p
= 0.004), mean transit time (2.88 vs. 4.88 s, p = 0.039),
and blood volume (1.9 vs. 0.7\%, p = 0.019). A
inversion-prepared dual-contrast sequence acquiring T (1)-
and [Formula: see text]-weighted images with sufficient
temporal resolution and signal-to-noise ratio was
successfully applied in patients with prostate cancer to
quantify all pharmacokinetic parameters of inflow and
extravasation of a low-molecular-weight inert tracer.},
keywords = {Dynamic contrast-enhanced magnetic resonance imaging;
Perfusion; Permeability; Dual contrast; Prostate},
doi = {10.1007/s10439-009-9645-x},
url = {http://www.springerlink.com/content/x17118h8008121j7},
pdf = {2009-luedemann-annbme-dynamic_ce_mri_prostate_perfusion_permeability.pdf},
pmid = 19169821,
pmc = {},
category = {journal}
}
@article{SullAdalRohl:2009,
author = {Sullivan, Edith V. and Adalsteinsson, Elfar and Rohlfing,
Torsten and Pfefferbaum, Adolf},
title = {Relevance of Iron Deposition in Deep Gray Matter Brain
Structures to Cognitive and Motor Performance in Healthy
Elderly Men and Women: Exploratory Findings},
journal = {Brain Imaging and Behavior},
year = 2009,
volume = 3,
number = 2,
pages = {167--175},
month = {Jun.},
abstract = {Iron deposition increases in normal aging, has its greatest
presence in structures of the extrapyramidal system, and may
contribute to functional decline. MR imaging provides a
method for indexing iron deposition in brain structures
because of iron’s ferromagnetic properties, which interact
with the MRI environment to cause signal intensity
attenuation that is quantifiable by comparing images
collected at 1.5 and 3.0 T. We tested functional correlates
of an MR-based iron index in 10 healthy, elderly individuals
previously reported to have a higher iron burden in the
putamen and lower in the thalamus than young
individuals. Lower scores on the Dementia Rating Scale and
longer reaction times on a two-choice attention test
correlated with higher iron estimates in the caudate nucleus
and putamen; poorer Mini-Mental State Examination and Digit
Symbol scores correlated with lower iron estimates in the
thalamus. Further analyses based on multiple regression,
which considered regional FDRI estimates and volume measures
as predictors of performance, identified iron but not the
sampled volume as the unique predictor in each case. These
exploratory correlations suggest a substrate of performance
degradation in aging and have implications for regional
signal darkening in an array of MR-based imaging
protocols.},
keywords = {Iron; Basal ganglia; Extrapyramidal system; Thalamus; MRI;
Cognition; Motor; Age; Aging},
doi = {10.1007/s11682-008-9059-7},
url = {http://www.springerlink.com/content/bu8166l451l02417/fulltext.html},
pdf = {2009-sullivan-bib-iron_deposition_deep_gm_cognitive_motor_performance.pdf},
pmc = {},
category = {journal}
}
@article{PfefRoseRohl:2009,
author = {Pfefferbaum, Adolf and Rosenbloom, Margaret and Rohlfing,
Torsten and Sullivan, Edith V.},
title = {Degradation of Selective Lateral and Interhemispheric Brain
White Matter Systems in Alcoholism Detected with
Quantitative Fiber Tracking},
journal = {Biological Psychiatry},
year = 2009,
volume = 65,
number = 8,
pages = {680--690},
month = {Apr.},
abstract = {BACKGROUND: Excessive alcohol use can cause macrostructural
tissue shrinkage with regional preference for frontal
systems. The extent and locus of alcoholism's effect on
white matter microstructure is less known. METHODS:
Quantitative fiber tracking derived from diffusion tensor
imaging (DTI) assessed the integrity of samples of 11 major
white matter bundles in 87 alcoholics (59 men, 28 women) and
88 healthy control subjects (42 men, 46 women). Fiber
integrity was expressed as fractional anisotropy (FA) and
apparent diffusion coefficient (ADC), quantified separately
for longitudinal diffusivity (lambdaL), a putative index of
axonal integrity, and transverse diffusivity (lambdaT), a
putative index of myelin integrity. RESULTS: Alcoholism
affected FA and diffusivity, particularly lambdaT, of
several fiber bundles. Frontal and superior sites (frontal
forceps, internal and external capsules, fornix, and
superior cingulate and longitudinal fasciculi) showed
greatest abnormalities in alcoholics relative to control
subjects. More posterior and inferior bundles were
relatively spared. Lifetime alcohol consumption correlated
with regional DTI measures in alcoholic men but not
women. When matched for alcohol exposure, alcoholic women
showed more DTI signs of white matter degradation than
alcoholic men in several fiber bundles. Among all
alcoholics, poorer performance on speeded tests correlated
with DTI signs of regional white matter
degradation. CONCLUSIONS: This survey of multiple brain
fiber systems revealed a differential pattern of
alcoholism's effect on regional FA and diffusivity with
functional consequences attributable in part to compromised
fiber microstructure with prominence in signs of myelin
degradation. Sex-based differences suggest that women are at
enhanced risk for alcoholism-related degradation in
selective white matter systems.},
keywords = {Alcoholism; brain; diffusion; DTI; fiber tracking; sex
differences; white matter},
doi = {10.1016/j.biopsych.2008.10.039},
pdf = {2009-pfefferbaum-biolpsych-degradation_wm_systems_alcoholism.pdf},
pmid = 19103436,
category = {journal}
}
@article{ZahrRohlPfef:2009,
author = {Zahr, Natalie M. and Rohlfing, Torsten and Pfefferbaum,
Adolf and Sullivan, Edith V.},
title = {Problem solving, working memory, and motor correlates of
association and commissural fiber bundles in normal aging: A
quantitative fiber tracking study},
journal = {NeuroImage},
year = 2009,
volume = 44,
number = 3,
pages = {1050--1062},
month = {Feb.},
abstract = {Normal aging is accompanied by decline in selective
cognitive and motor functions. A concurrent decline in
regional white matter integrity, detectable with diffusion
tensor imaging (DTI), potentially contributes to waning
function. DTI analysis of white matter loci indicates an
anterior-toposterior gradient distribution of declining
fractional anisotropy (FA) and increasing diffusivity with
age. Quantitative fiber tracking can be used to determine
regional patterns of normal aging of fiber systems and test
the functional ramifications of the DTI metrics. Here, we
used quantitative fiber tracking to examine age effects on
commissural (genu and splenium), bilateral association
(cingulate, inferior longitudinal fasciculus and uncinate),
and fornix fibers in 12 young and 12 elderly healthy men and
women and tested functional correlates with concurrent
assessment of a wide range of neuropsychological
abilities. Principal component analysis of cognitive and
motor tests on which the elderly achieved significantly
lower scores than the young group was used for data
reduction and yielded three factors: Problem Solving,
Working Memory, and Motor. Age effects -- lower FA or higher
diffusivity -- in the elderly were prominent in anterior
tracts, specifically, genu, fornix, and uncinate
fibers. Differential correlations between FA or diffusivity
in fiber tracts and scores on Problem Solving, Working
Memory, or Motor factors provide convergent validity to the
biological meaningfulness of the integrity of the fibers
tracked. The observed pattern of relations supports the
possibility that regional degradation of white matter fiber
integrity is a biological source of age-related functional
compromise and may have the potential to limit accessibility
to alternative neural systems to compensate for compromised
function.},
keywords = {Fiber tracking; White matter; DTI; Cognition; Motor; Problem
solving; Working memory; Age},
doi = {10.1016/j.neuroimage.2008.09.046},
pdf = {2009-zahr-nimg-problem_solving_working_memory_motor_aging_fiber_tracking.pdf},
pmid = 18977450,
category = {journal}
}
@article{AmthRufBoeh:2004,
author = {Amthauer, Holger and Ruf, Juri and B\"ohmig, Michael and
Lopez-H\"anninen, Enrique and Rohlfing, Torsten and Wernecke,
K.-D. and Pl\"ockinger, U. and Gutberlet, Matthias and
Lemke, Arne-J\"orn and Steinm\"uller, T. and Wiedenmann,
B. and Felix, Roland},
title = {Diagnostics of Neuroendocrine Tumors by Retrospective Image
Fusion: Is there a Benefit?},
journal = {European Journal of Nuclear Medicine},
year = 2004,
volume = 31,
number = 3,
pages = {342--348},
month = {Mar.},
abstract = {This study evaluated the use of image fusion in the
preoperative staging of neuroendocrine tumors (NET) of the
pancreas and the gastrointestinal tract (GIT). Thirty-eight
patients suffering from a metastasized NET with location of
the primary in the pancreas (n=15) or the GIT (n=23) were
examined by somatostatin receptor scintigraphy (SRS) and
computed tomography (CT). Consecutive image registration and
fusion were performed using custom-built software integrated
in AVS/Express (Advanced Visual Systems, Waltham, MA,
USA). Registration was performed by a voxel-based algorithm
based on normalized mutual information. Image fusion was
feasible in 36/38 patients. A total of 87 foci were assigned
to anatomical regions (e.g. gut, pancreas, liver, lymph node
or others) by two independent observers in both SRS and
SRS/CT fusion images. The assignments used a binary ranking
system (1=definite, 0=not definite). These results were then
retrospectively compared to the classification of the foci,
based on postoperative histology or clinical
follow-up. Imaging by SRS allowed a definite anatomical
assignment in 57\% (50/87) and 61\% (53/87) of all lesions
in the case of observers A and B, respectively. Image fusion
improved the topographic assignment to 91\% (79/87) and to
93\% (81/87). The number classified as definite by both
observers increased from 54\% (47/87) to 86\% (77/87). The
increase in definite assignments was highly significant for
both observers (P<0.0001 for each). In the case of foci
classified as liver metastases, image fusion allowed
improved assignment to the corresponding liver segment from
45\% (18/40) to 98\% (39/40) and from 58\% (23/40) to 100\%
(40/40) by observers A and B, respectively. Furthermore, the
improved assignment of foci classified as lesions by image
fusion was relevant for therapy in 7/36 patients
(19\%). Therefore, the image fusion technique presented
herein appears to be a very useful method for clinical
routine.},
keywords = {Neuroendocrine tumors; Somatostatin receptor scintigraphy;
Computed tomography; Image registration; Image fusion},
doi = {10.1007/s00259-003-1379-7},
pdf = {2004-amthauer-ejnm-endocrine_tumors_fusion.pdf},
url = {http://springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s00259-003-1379-7},
copyright = {Copyright to this article is owned by Springer-Verlag. The
original publication is available at springerlink.com},
category = {journal},
pmid = {14652697}
}
@article{BranRohlRyba:2005,
author = {Brandt, Robert and Rohlfing, Torsten and Rybak, J\"urgen and
Krofczik, Sabine and Maye, Alexander and Westerhoff, Malte
and Hege, Hans-Christian and Menzel, Randolf},
title = {Three-dimensional average-shape atlas of the honeybee brain
and its applications},
year = 2005,
journal = {Journal of Comparative Neurology},
volume = 492,
number = 1,
pages = {1--19},
month = {Nov.},
abstract = {The anatomical substrates of neural nets are usually
composed from reconstructions of neurons that were stained
in different preparations. Realistic models of the
structural relationships between neurons require a common
framework. Here we present 3-D reconstructions of single
projection neurons (PN) connecting the antennal lobe (AL)
with the mushroom body (MB) and lateral horn, groups of
intrinsic mushroom body neurons (type 5 Kenyon cells), and a
single mushroom body extrinsic neuron (PE1), aiming to
compose components of the olfactory pathway in the
honeybee. To do so, we constructed a digital standard atlas
of the bee brain. The standard atlas was created as an
average-shape atlas of 22 neuropils, calculated from 20
individual immunostained whole-mount bee brains. After
correction for global size and positioning differences by
repeatedly applying an intensity-based nonrigid registration
algorithm, a sequence of average label images was
created. The results were qualitatively evaluated by
generating average gray-value images corresponding to the
average label images and judging the level of detail within
the labeled regions. We found that the first affine
registration step in the sequence results in a blurred image
because of considerable local shape differences. However,
already the first nonrigid iteration in the sequence
corrected for most of the shape differences among
individuals, resulting in images rich in internal detail. A
second iteration improved on that somewhat and was selected
as the standard. Registering neurons from different
preparations into the standard atlas reveals 1) that the
m-ACT neuron occupies the entire glomerulus (cortex and
core) and overlaps with a local interneuron in the cortical
layer; 2) that, in the MB calyces and the lateral horn of
the protocerebral lobe, the axon terminals of two identified
m-ACT neurons arborize in separate but close areas of the
neuropil; and 3) that MB-intrinsic clawed Kenyon cells (type
5), with somata outside the calycal cups, project to the
peduncle and lobe output system of the MB and contact
(proximate) the dendritic tree of the PE1 neuron at the base
of the vertical lobe. Thus the standard atlas and the
procedures applied for registration serve the function of
creating realistic neuroanatomical models of parts of a
neural net. The Honeybee Standard Brain is accessible at
www.neurobiologie.fu-berlin.de/beebrain.},
keywords = {virtual neuroanatomy; insect brain; brain atlas; brain
reference system; mushroom bodies; antennal lobe; olfactory
system},
doi = {10.1002/cne.20644},
pdf = {2005-brandt-jcn-average_shape_atlas_honeybee_brain.pdf},
category = {journal},
url = {http://dx.doi.org/10.1002/cne.20644},
pmid = {16175557}
}
@article{CitaGallBatr:2004,
author = {Citardi, Martin J. and Gallivan, Ryan P. and Batra, Pete and
Maurer, Jr., Calvin R. and Rohlfing, Torsten and Roh,
Hwan-Jung and Lanza, Donald C.},
title = {Quantitative Computer-Aided {CT} Analysis of Sphenoid Sinus
Anatomical Relationships},
journal = {American Journal of Rhinology},
year = 2004,
category = {journal},
volume = 18,
number = 3,
pages = {173--178},
month = {Jun.},
abstract = {Background: This study describes a novel computer-generated
anatomic symmetry plane as a framework for the quantitative
description of sphenoid sinus anatomy. The aim of this study
was to (1) determine relationships and distances between a
midline sphenoid reference point (called the central
sphenoid point [CSP]) and lateral sphenoid wall structures
and (2) assess the incidence of anterior clinoid process
(ACP) pneumatization and pterygoid recess (PR)
pneumatization.
Methods: Axial computed tomography (CT) scans (1-mm slice
thickness) were obtained on a VolumeZoom CT scanner (Siemens
Medical, Erlangen, Germany). Mathematically derived anatomic
symmetry planes were created using custom postprocessing
software. A standardized review of each CT scan using
surgical planning software (CBYON Suite version 2.6; CBYON,
Mountain View, CA) was performed. The CSP was defined as a
reference point in the midline sagittal plane at the
intersection of the vertical sellar face and the horizontal
sellar floor.
Results: A total of 128 sides in 64 cadaveric specimens were
available for review. The incidences of ACP pneumatization
and PR pneumatization were 23.4 and 37.5\%. The mean
distances from the CSP to the left optic canal midpoint, the
left ACP entrance point, and the left PR lateral wall were
17.2, 15.6, and 27.6 mm, respectively. The corresponding
distances from the CSP on the right side were 17.3, 15.8,
and 28.0 mm, respectively. Measurements from the maxillary
spine to the optic canal midpoint, ACP entrance point, and
PR lateral wall on each side were performed also.
Conclusion: This approach provides both quantitative and
qualitative understanding of sphenoid osteology and may be
coupled with intraoperative surgical navigation to reduce
the risks of sphenoid surgery. Both PR and ACP
pneumatization are surprisingly common. Because the
CSP-derived relationships may be referenced during
endoscopic surgical navigation, they may provide greater
clinical utility than traditional alternatives. This
paradigm may facilitate a greater understanding of sphenoid
anatomy and enhance surgical safety and precision.},
keywords = {symmetry; ENT},
pdf = {2004-citardi-ajr-sphenoid_sinus.pdf},
pmid = {15283492},
issn = {1050-6586},
url = {http://thesius.ingentaselect.com/vl=3843347/cl=42/nw=1/rpsv/cw/ocean/10506586/v18n3/s8/p173}
}
@article{GiroRohlMaur:2008,
author = {Girod, Sabine and Rohlfing, Torsten and Maurer, Jr., Calvin
R.},
title = {Imaging and Intraoperative Guidance in Implant-Based
Auricular Reconstruction},
journal = {Journal of Oral and Maxillofacial Surgery},
year = 2008,
volume = 66,
number = 6,
pages = {1302--1306},
month = {Jun.},
doi = {10.1016/j.joms.2007.06.636},
pdf = {2008-girod-joms-igs_navigation_auricular_implant.pdf},
pmid = 18486803,
url = {http://www.sciencedirect.com/science/article/B6WKF-4SJYSPC-1C/1/9d3af48165812e2cf34561ed04047d11},
category = {journal}
}
@article{KuryRohlKrof:2008,
author = {Kurylas, Angela E. and Rohlfing, T. and Krofczik, Sabine and
Jenett, Arnim and Homberg, Uwe},
title = {Standardized atlas of the brain of the desert locust,
Schistocerca gregaria},
journal = {Cell and Tissue Research},
year = 2008,
volume = 333,
number = 1,
pages = {125-145},
month = {Jul.},
abstract = {In order to understand the connectivity of neuronal
networks, their constituent neurons should ideally be
studied in a common framework. Since morphological data from
physiologically characterized and stained neurons usually
arise from different individual brains, this can only be
performed in a virtual standardized brain that compensates
for interindividual variability. The desert locust,
Schistocerca gregaria, is an insect species used widely for
the analysis of olfactory and visual signal processing,
endocrine functions, and neural networks controlling motor
output. To provide a common multi-user platform for neural
circuit analysis in the brain of this species, we have
generated a standardized three-dimensional brain of this
locust. Serial confocal images from whole-mount locust
brains were used to reconstruct 34 neuropil areas in ten
brains. For standardization, we compared two different
methods: an iterative shape-averaging (ISA) procedure by
using affine transformations followed by iterative nonrigid
registrations, and the Virtual Insect Brain (VIB) protocol
by using global and local rigid transformations followed by
local nonrigid transformations. Both methods generated a
standard brain, but for different applications. Whereas the
VIB technique was designed to visualize anatomical
variability between the input brains, the purpose of the ISA
method was the opposite, i.e., to remove this variability. A
novel individually labeled neuron, connecting the lobula to
the midbrain and deutocerebrum, has been registered into the
ISA atlas and demonstrates its usefulness and accuracy for
future analysis of neural networks. The locust standard
brain is accessible at http://www.3d-insectbrain.com.},
keywords = {Virtual Insect Brain protocol; Iterative shape averaging;
Three-dimensional reconstruction; Standard brain; Virtual
neuroanatomy; Schistocerca gregaria (Insecta)},
doi = {10.1007/s00441-008-0620-x},
pdf = {2008-kurylas-ctr-desert_locust_standard_brain_atlas.pdf},
pmid = 18504618,
url = {http://www.springerlink.com/index/10.1007/s00441-008-0620-x},
category = {journal}
}
@article{HoldHillDent:2000,
author = {Holden, Mark and Hill, Derek L.~G. and Denton, Erika
R.~E. and Jarosz, Jo M. and Cox, Tim C.~S. and Rohlfing,
Torsten and Goodey, Joanne and Hawkes, David J.},
title = {Voxel Similarity Measures for {3-D} Serial {MR} Brain Image
Registration},
journal = {IEEE Transactions on Medical Imaging},
year = 2000,
volume = 19,
number = 2,
pages = {94--102},
month = {Feb.},
abstract = {The authors have evaluated eight different similarity
measures used for rigid body registration of serial magnetic
resonance (MR) brain scans. To assess their accuracy the
authors used 33 clinical three-dimensional (3-D) serial MR
images, with deformable extradural tissue excluded by manual
segmentation and simulated 3-D MR images with added
intensity distortion. For each measure the authors
determined the consistency of registration transformations
for both sets of segmented and unsegmented data. They have
shown that of the eight measures tested, the ones based on
joint entropy produced the best consistency. In particular,
these measures seemed to be least sensitive to the presence
of extradural tissue. For these data the difference in
accuracy of these joint entropy measures, with or without
brain segmentation, was within the threshold of visually
detectable change in the difference images.},
keywords = {biomedical MRI; brain; entropy; image registration; image
segmentation; medical image processing; 3-D serial MR brain
image registration; MRI; brain segmentation; extradural
tissue; joint entropy; magnetic resonance imaging; medical
diagnostic imaging; transformation estimates consistency;
voxel similarity measures},
pdf = {2000-holden-tmi-serial_brain_registration.pdf},
pmid = {10784281},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isNumber=18064&prod=JNL&arnumber=836369&arSt=94&ared=102&arAuthor=Holden%2C+M.%3B+Hill%2C+D.L.G.%3B+Denton%2C+E.R.E.%3B+Jarosz%2C+J.M.%3B+Cox%2C+T.C.S.%3B+Rohlfing%2C+T.%3B+Goodey%2C+J.%3B+Hawkes%2C+D.J.&arNumber=836369&a_id0=836367&a_id1=836368&a_id2=836369&a_id3=836370&a_id4=836371&a_id5=836372&a_id6=836373&count=7},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
category = {journal}
}
@article{HostKreiPuls:2000,
author = {Hosten, Norbert and Kreissig, Roland and Puls, Ralf and
Amthauer, Holger and Beier, J\"urgen and Rohlfing, Torsten
and Stroszczynski, Christian and Herbel, A. and Lemke,
Arne-J\"orn and Felix, Roland},
title = {Fusion of {CT} and {PET} data: Methods and clinical
relevance for planning laser-induced thermotherapy of liver
metastases},
journal = {Fortschr R\"ontgenstr},
year = 2000,
volume = 172,
number = 7,
pages = {630--635},
month = {Jul.},
abstract = {Aim: Catheter-placement in liver metastases is difficult
when the lesions are not visible on plain images. We
evaluated the use of image fusion using CT and PET data,
providing information on anatomy and liver lesions,
respectively. Methods: Plain CT of the liver and whole body
FDG-PET were performed in 28 patients with colorectal
carcinoma in preparation for laser-induced
thermotherapy. Fusions of image data and 2D-visualisation
were performed and evaluated with regard to quality of the
registration, number of detected lesions and influence of
the procedure on laser-induced thermotherapy. Image fusion
was performed using an algorithm which was developed by our
group. Results: 84 focal liver lesions were visible on CT,
107 on PET images. This means that CT guided catheter
placement would have to be performed "blindly" in 23
lesions. In 6 patients previously unknown extra-hepatic
tumor deposits were seen on PET images (local recurrence, 2
extrahepatic metastases, 2 second primaries). Conclusion:
Hot spots from metastases, which are difficult to locate on
PET images alone, may be identified on images generated by
fusion of CT and PET data. These images facilitate an
interventional approach to liver lesions which are not
visible on plain CT. As PET allows for whole body screening,
it helps identifying patients who would not profit from
laser-induced thermotherapy.},
pdf = {2000-hosten-roefo-ct_pet_fusion_litt_liver_metastases.pdf},
keywords = {Image fusion - Laser-induced interstitial thermotherapy
(LITT) - Computed tomography (CT) - Magnetic resonance
imaging (MRI) - Positron emission tomography (PET) - Liver
metastases},
pmid = {10962990},
category = {journal},
copyright = {Copyright for this paper is owned by Thieme. The original
paper is available from www.thieme-connect.com.}
}
@article{JeffPottChan:2007,
author = {Jefferis, Gregory S.X.E. and Potter, Christopher J. and
Chan, Alexander M. and Marin, Elizabeth C. and Rohlfing,
Torsten and Maurer, Jr., Calvin R. and Luo, Liqun},
title = {Comprehensive Maps of {{\em Drosophila\/}} Higher Olfactory
Centers: Spatially Segregated Fruit and Pheromone
Representation},
journal = {Cell},
year = 2007,
volume = 128,
number = 6,
pages = {1187--1203},
month = {Mar.},
abstract = {In {\em Drosophila\/}, $\approx$50 classes of olfactory
receptor neurons (ORNs) send axons to 50 corresponding
glomeruli in the antennal lobe. Uniglomerular projection
neurons (PNs) relay olfactory information to the mushroom
body (MB) and lateral horn (LH). Here, we combine
single-cell labeling and image registration to create
high-resolution, quantitative maps of the MB and LH for 35
input PN channels and several groups of LH neurons. We find
(1) PN inputs to the MB are stereotyped as previously shown
for the LH; (2) PN partners of ORNs from different sensillar
groups are clustered in the LH; (3) fruit odors are
represented mostly in the posterior-dorsal LH, whereas
candidate pheromone-responsive PNs project to the
anterior-ventral LH; (4) dendrites of single LH neurons each
overlap with specific subsets of PN axons. Our results
suggest that the LH is organized according to biological
values of olfactory input.},
category = {journal},
url = {http://www.cell.com/content/article/abstract?uid=PIIS0092867407002048},
pmid = {17382886},
pmc = {1885945},
pdf = {2007-jefferis-cell-olfactory_mapping_drosophila.pdf}
}
@article{LemkNiehAmth:2004,
author = {Lemke, Arne-J\"orn and Niehues, Stefan M. and Amthauer,
Holger and Rohlfing, Torsten and Hosten, Norbert and Felix,
Roland},
title = {{Klinischer Einsatz der digitalen retrospektiven Bildfusion
von CT, MRT, FDG-PET und SPECT - Anwendungsgebiete und
Ergebnisse} [{Clinical} Use of Digital Retrospective Image
Fusion of {CT}, {MRI}, {FDG}-{PET} and {SPECT} - Fields of
Indications and Results]},
journal = {Fortschr R\"ontgenstr},
year = 2004,
volume = 176,
number = 12,
pages = {1811--1818},
month = {Dec.},
note = {article in German},
abstract = {PURPOSE: To evaluate the feasibility and the clinical
benefits of retrospective digital image fusion (PET, SPECT,
CT and MRI). MATERIALS AND METHODS: In a prospective study,
a total of 273 image fusions were performed and
evaluated. The underlying image acquisitions (CT, MRI, SPECT
and PET) were performed in a way appropriate for the
respective clinical question and anatomical region. Image
fusion was executed with a software program developed during
this study. The results of the image fusion procedure were
evaluated in terms of technical feasibility, clinical
objective, and therapeutic impact. RESULTS: The most
frequent combinations of modalities were CT/PET (n = 156)
and MRI/PET (n = 59), followed by MRI/SPECT (n = 28),
CT/SPECT (n = 22) and CT/MRI (n = 8). The clinical questions
included following regions (more than one region per case
possible): neurocranium (n = 42), neck (n = 13), lung and
mediastinum (n = 24), abdomen (n = 181), and pelvis (n =
65). In 92.6\% of all cases (n = 253), image fusion was
technically successful. Image fusion was able to improve
sensitivity and specificity of the single modality, or to
add important diagnostic information. Image fusion was
problematic in cases of different body positions between the
two imaging modalities or different positions of mobile
organs. In 37.9\% of the cases, image fusion added
clinically relevant information compared to the single
modality. CONCLUSION: For clinical questions concerning
liver, pancreas, rectum, neck, or neurocranium, image fusion
is a reliable method suitable for routine clinical
application. Organ motion still limits its feasibility and
routine use in other areas (e. g., thorax).},
keywords = {Retrospective image fusion; CT; MRI; PET; SPECT;
differential diagnosis},
doi = {10.1055/s-2004-813663},
category = {journal},
pdf = {2004-lemke-roefo-bildfusion.pdf},
pmid = {15573293},
url = {http://www.thieme-connect.de/ejournals/abstract/roefo/doi/10.1055/s-2004-813663},
copyright = {Copyright for this paper is owned by Thieme. The original
paper is available from www.thieme-connect.com.}
}
@article{LemkNiehHost:2004,
author = {Lemke, Arne-J\"o{}rn and Niehues, Stefan Markus and Hosten,
Norbert and Amthauer, Holger and Boehmig, Michael and
Stroszczynski, Christian and Rohlfing, Torsten and Rosewicz,
Stefan and Felix, Roland},
title = {Retrospective Digital Image Fusion of Multidetector {CT} and
{18F}-{FDG} {PET}: Clinical Value in Pancreatic Lesions -- A
Prospective Study with 104 Patients},
journal = {Journal of Nuclear Medicine},
year = 2004,
volume = 45,
number = 8,
month = {Aug.},
pages = {1279--1286},
abstract = {Differential diagnosis of pancreatic lesions still remains a
problem. Whereas CT provides high spatial resolution, PET
detects malignant lesions with high sensitivity. The
objective of this study was to evaluate the clinical benefit
of PET/CT image fusion in the diagnostic workup of
pancreatic cancer. Methods: One hundred four patients with
suspected pancreatic lesion underwent triple-phase
multidetector CT and 18F-FDG PET scanning. Voxel-based
retrospective registration and fusion of CT and PET were
performed with recently developed software. CT, PET, and
fused images were assessed by 2 radiologists with regard to
the detection of malignancies, possible infiltration of
adjacent tissue or lymph nodes, or distant
metastases. Results: Fusion of CT and PET images was
technically successful in 96.2\%. In 2 cases, paraaortic
lymph node infiltration was detected only by image fusion;
in a further 8 cases, lymph node metastases were confirmed
with improved localization. In 5 patients, additional
pancreatic tumors or distant metastases only suspected
during PET scanning were confirmed. Image fusion improved
the sensitivity of malignancy detection from 76.6\% (CT) and
84.4\% (PET) to 89.1\% (image fusion). Compared with CT
alone, image fusion increased the sensitivity of detecting
tissue infiltration to 68.2\%, but at the cost of decreased
specificity. Conclusion: The most important supplementary
finding supplied by image fusion is a more precise
correlation with focal tracer hot spots in PET. Image fusion
improved the sensitivity of differentiating between benign
and malignant pancreatic lesions with no significant change
in specificity. All image modalities failed to stage lymph
node involvement.},
keywords = {PET; CT, spiral; image manipulation or reconstruction;
pancreas; computer applications, detection},
pdf = {2004-lemke-jnm-CT_PET_fusion_pancreas.pdf},
url = {http://jnm.snmjournals.org/cgi/content/full/45/8/1279},
pmid = {15299049},
copyright = {Copyright to this article is owned by the Society of
Nuclear Medicine. The original publication is available at
jnm.snmjournals.org},
category = {journal}
}
@article{PfefAdalRohl:2009,
author = {Pfefferbaum, Adolf and Adalsteinsson, Elfar and Rohlfing,
Torsten and Sullivan, Edith V.},
title = {Diffusion tensor imaging of deep gray matter brain
structures: Effects of age and iron concentration},
journal = {Neurobiology of Aging},
year = {2009},
volume = { },
number = { },
pages = {in press},
month = { },
abstract = {Diffusion tensor imaging (DTI) of the brain has become a
mainstay in the study of normal aging of white matter, and
only recently has attention turned to the use of DTI to
examine aging effects in gray matter structures. Of the many
changes in the brain that occur with advancing age is
increased presence of iron, notable in selective deep gray
matter structures. In vivo detection and measurement of iron
deposition is possible with magnetic resonance imaging (MRI)
because of iron's effect on signal intensity. In the process
of a DTI study, a series of diffusion-weighted images (DWI)
is collected, and while not normally considered as a major
dependent variable in research studies, they are used
clinically and they reveal striking conspicuity of the
globus pallidus and putamen caused by signal loss in these
structures, presumably due to iron accumulation with
age. These iron deposits may in turn influence DTI metrics,
especially of deep gray matter structures. The combined
imaging modality approach has not been previously used in
the study of normal aging. The present study used legacy DTI
data collected in 10 younger (22-37 years) and 10 older
(65-79 years) men and women at 3.0 T and fast spin-echo
(FSE) data collected at 1.5 T and 3.0 T to derive an
estimate of the field-dependent relaxation rate increase
(the ``FDRI estimate'') in the putamen, caudate nucleus,
globus pallidus, thalamus, and a frontal white matter sample
comparison region. The effect of age on the diffusion
measures in the deep gray matter structures was distinctly
different from that reported in white matter. In contrast to
lower anisotropy and higher diffusivity typical in white
matter of older relative to younger adults observed with
DTI, both anisotropy and diffusivity were higher in the
older than younger group in the caudate nucleus and putamen;
the thalamus showed little effect of age on anisotropy or
diffusivity. Signal intensity measured with DWI was lower in
the putamen of elderly than young adults, whereas the
opposite was observed for the white matter region and
thalamus. As a retrospective study based on legacy data, the
FDRI estimates were based on FSE sequences, which
underestimated the classical FDRI index of brain
iron. Nonetheless, the differential effects of age on DTI
metrics in subcortical gray matter structures compared with
white matter tracts appears to be related, at least in part,
to local iron content, which in the elderly of the present
study was prominent in the FDRI estimate of the putamen and
visibly striking in the diffusion-weighted image of the
basal ganglia structures.},
keywords = {Brain; Aging; Iron; DTI; DWI; MRI; Diffusion},
doi = {10.1016/j.neurobiolaging.2008.04.013 },
pdf = { },
category = {journal},
pmid = 18513834
}
@article{PfefRoseRohl:2006,
author = {Pfefferbaum, Adolf and Rosenbloom, Margaret J. and Rohlfing,
Torsten and Adalsteinsson, Elfar and Kemper, Carol A. and
Deresinski, Stanley and Sullivan, Edith V.},
title = {Contribution of alcoholism to brain dysmorphology in {HIV}
infection: Effects on the ventricles and corpus callosum},
journal = {NeuroImage},
year = 2006,
volume = 33,
number = 1,
pages = {239--251},
month = {Oct.},
abstract = {Nonrigid registration and atlas-based parcellation methods
were used to compare the volume of the ventricular system
and the cross-sectional area of the midsagittal corpus
callosum on brain MRIs from 272 subjects in four groups:
patients with HIV infection, with and without alcoholism
comorbidity, alcoholics, and controls. Prior to testing
group differences in regional brain metrics, each measure
was corrected by regression analysis for significant
correlations with supratentorial cranial volume and age,
observed in 121 normal control men and women, whose age
spanned six decades. Disregarding HIV disease severity, we
observed a graded pattern of modest enlargement of the total
ventricular system (0.28 SD for uncomplicated HIV, 0.65 SD
for HIV comorbid with alcoholism, and 0.72 SD for the
alcoholism group). The pattern of callosal thinning showed a
similar but small ($\approx$0.5 SD) graded effect. A
different pattern emerged, however, when HIV severity in the
context of alcoholism comorbidity was factored into the
analysis. Substantially greater volume abnormalities were
present in individuals with a history of an AIDS-defining
event or low CD4+ T cell counts ($\le$200 mm\textsupthree{})
irrespective of alcoholism comorbidity, and the effect of
HIV severity was disproportionately exacerbated by
alcoholism comorbidity, with 1 SD size deficit in the genu
of corpus callosum and nearly 2 SD greater volume of the
frontal and body regions of the ventricles for the AIDS +
alcohol comorbid group. The differences in brain volumes
between the AIDS groups with vs. without alcoholism could
not be attributed to differences in HIV disease severity,
defined by CD4+ count, viral load, or Karnofsky score. The
substantial effect of the alcoholism--AIDS interaction on
ventricular and callosal dysmorphology, in the context of
the modest changes observed in non-AIDS, nonalcohol abusing
HIV-infected individuals, highlight the need to consider
alcohol use disorders as a major risk factor for
neuropathology among HIV-infected persons.},
doi = {10.1016/j.neuroimage.2006.05.052},
category = {journal},
url = {http://www.sciencedirect.com/science/article/B6WNP-4KJ0SPV-2/2/b558fa3f6c143b6c8639b73c9afbe23c},
pdf = {2006-pfefferbaum-neuroimage-alcoholism_hiv_ventricles_cc.pdf},
pmid = {16877010}
}
@article{PfefZahrMaye:2008,
author = {Pfefferbaum, Adolf and Zahr, Natalie M. and Mayer, Dirk and
Vinco, Shara and Orduna, Juan and Rohlfing, Torsten and
Sullivan, Edith V.},
title = {Ventricular Expansion in Wild-Type {Wistar} Rats after
Alcohol Exposure by Vapor Chamber},
journal = {Alcoholism: Clinical and Experimental Research},
year = 2008,
volume = 32,
number = 8,
pages = {1459--1467},
month = {Aug.},
abstract = {Background: Structural magnetic resonance imaging (MRI)
reveals widespread brain damage manifest as tissue shrinkage
and complementary ventriculomegaly in human alcoholism. For
an animal model to parallel the human condition, high
alcohol exposure should produce similar radiologically
detectable neuropathology. Our previous structural MRI study
demonstrated only modest brain dysmorphology of the
alcohol-preferring (P) rat with average blood alcohol levels
(BALs) of 125 mg/dl achieved with voluntary
consumption. Here, we tested the hypothesis that wild-type
Wistar rats, exposed to vaporized alcohol ensuring higher
BALs than typically achieved with voluntary consumption in
rodents, would model MRI findings in the brains of humans
with chronic alcoholism.
Methods: The longitudinal effects of vaporized alcohol
exposure on the brains of 10 wild-type Wistar rats compared
with 10 sibling controls were investigated with structural
MRI, conducted before (MRI 1) and after (MRI 2) 16 of
alcohol exposure and after an additional 8 weeks at a higher
concentration of alcohol (MRI 3).
Results: Two rats in the alcohol group died prior to MRI
2. The remaining vapor-exposed rats (n = 8) achieved BALs of
293 mg/dl by MRI 2 and 445 mg/dl by MRI 3. Whereas the
controls gained 17\% of their body weight from MRI 1 to MRI
3, the alcohol-exposed group lost 6\%. MRI, quantified with
atlas-based parcellation, revealed a profile of significant
ventricular expansion, after alcohol vapor exposure, in 9
contiguous slices, extending from the dorsolateral to
ventrolateral ventricles. In particular, from MRI 1 to MRI
2, this ventricular volume expanded by an average of 6.5\%
in the controls and by 27.1\% in the alcohol-exposed rats
but only an additional 1.5\% in controls and 2.4\% in
alcohol-exposed rats from MRI 2 to MRI 3. The midsagittal
volume of the full anterior-to-posterior extent of the
corpus callosum grew between the first 2 MRIs in both groups
followed by regression in the alcohol group by MRI
3. Although group differences were statistically
significant, among animals there was substantial variability
of the effects of alcohol exposure on brain morphology; some
animals showed profound effects, whereas others were
essentially unaffected.
Conclusions: The ventricular dilatation and callosal
shrinkage produced in wild-type rats following involuntary
alcohol exposure yielded a modestly successful model of
neurodysmorphology phenotypes of human alcoholism. As is the
case for the human condition, however, in which some
individuals express greater alcoholism-related
neuropathology than others, some rats may be more
susceptible than others to extreme alcohol exposure.},
keywords = {Alcohol; Rat; Magnetic Resonance Imaging; Vaporized Alcohol;
Brai;, Corpus Callosum; Ventricles},
doi = {10.1111/j.1530-0277.2008.00721.x},
pmid = {18798357},
pmc = {2651956},
pdf = {2008-pfefferbaum-acer-ventricular_expansion_wistar_rats_vapor_chamber.pdf},
url = {http://www3.interscience.wiley.com/journal/120776454/abstract},
category = {journal}
}
@article{PohlBouiNaka:2007,
author = {Pohl, Kilian M. and Bouix, Sylvain and Nakamura, Motoaki and
Rohlfing, Torsten and McCarley, Robert W. and Kikinis, Ron
and Grimson, W. Eric L. and Shenton, Martha E. and Wells,
William M.},
title = {A Hierarchical Algorithm for {MR} Brain Image Parcellation},
journal = {IEEE Transactions on Medical Imaging},
year = 2007,
volume = 26,
number = 9,
pages = {1201--1212},
month = {Sep.},
abstract = {We introduce an algorithm for segmenting brain magnetic
resonance (MR) images into anatomical compartments such as
the major tissue classes and neuro-anatomical structures of
the gray matter. The algorithm is guided by prior
information represented within a tree structure. The tree
mirrors the hierarchy of anatomical structures and the
sub-trees correspond to limited segmentation problems. The
solution to each problem is estimated via a conventional
classifier. Our algorithm can be adapted to a wide range of
segmentation problems by modifying the tree structure or
replacing the classifier. We evaluate the performance of our
new segmentation approach by revisiting a previously
published statistical group comparison between first-episode
schizophrenia patients, first-episode affective psychosis
patients, and comparison subjects. The original study is
based on 50 MR volumes in which an expert identified the
brain tissue classes as well as the superior temporal gyrus,
amygdala, and hippocampus. We generate analogous
segmentations using our new method and repeat the
statistical group comparison. The results of our analysis
are similar to the original findings, except for one
structure (the left superior temporal gyrus) in which a
trend-level statistical significance (p=0.07) was observed
instead of statistical significance.},
keywords = {Automatic Segmentation; Data Tree; Expectation-Maximization;
Parcellation; Statistical Group Comparison Study; MRI},
doi = {10.1109/TMI.2007.901433},
pmid = {17896593},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4298155&isnumber=4298140},
pdf = {2007-pohl-tmi-hierarchical_mr_brain_image_parcellation.pdf},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
category = {journal}
}
@article{RohlBranMenz:2004a,
author = {Rohlfing, Torsten and Brandt, Robert and Menzel, Randolf and
Maurer, Jr., Calvin R.},
title = {Evaluation of Atlas Selection Strategies for Atlas-Based
Image Segmentation with Application to Confocal Microscopy
Images of Bee Brains},
abstract = {This paper evaluates strategies for atlas selection in
atlas-based segmentation of three-dimensional biomedical
images. Segmentation by intensity-based non-rigid
registration to atlas images is applied to confocal
microscopy images acquired from the brains of 20 bees. This
paper evaluates and compares four different approaches for
atlas image selection: registration to an individual atlas
image (IND), registration to an average shape atlas image
(AVG), registration to the most similar image from a
database of individual atlas images (SIM), and registration
to all images from a database of individual atlas images
with subsequent multi-classifier decision fusion (MUL). The
MUL strategy is a novel application of multi-classifier
techniques, which are common in pattern recognition, to
atlas-based segmentation. For each atlas selection strategy,
the segmentation performance of the algorithm was quantified
by means of the similarity index between the automatic
segmentation result and a manually generated gold
standard. The best segmentation accuracy was achieved using
the MUL paradigm, which resulted in a mean similarity index
value between manual and automatic segmentation of 0.86
(AVG, 0.84; SIM, 0.82; IND, 0.81). The superiority of the
MUL paradigm is statistically significant (two-sided paired
t-test, P<0.001). Our findings show that atlas selection is
an important issue in atlas-based segmentation and that in
particular multi-classifier techniques can substantially
increase the segmentation accuracy.},
keywords = {Atlas-based segmentation; Atlas selection; Non-rigid image
registration; Bee brain; Confocal microscopy imaging},
doi = {10.1016/j.neuroimage.2003.11.010},
pdf = {2004-rohlfing-nimg-atlas_selection.pdf},
journal = {NeuroImage},
volume = 21,
number = 4,
pages = {1428--1442},
month = {Apr.},
year = 2004,
category = {journal},
copyright = {Copyright for this paper is owned by Elsevier. The original
paper is available from sciencedirect.com. A preprint
version is available here.},
pmid = {15050568},
url = {http://www.sciencedirect.com/science/article/B6WNP-4BS0F4N-1/2/3452c4a5336f3edc4eb47d0e98f88163}
}
@article{RohlDenzGrae:2005,
author = {Rohlfing, Torsten and Denzler, Joachim and Gr\"a\ss{}l,
Christoph and Russakoff, Daniel B. and Maurer, Jr., Calvin
R.},
title = {Markerless real-time {3D} target region tracking by motion
backprojection from {2D} projection images},
journal = {IEEE Transactions on Medical Imaging},
year = 2005,
volume = 24,
number = 11,
pages = {1455--1468},
month = {Nov.},
abstract = {Accurate and fast localization of a pre-defined target
region inside the patient is an important component of many
image-guided therapy procedures. This problem is commonly
solved by registration of intra-operative 2D projection
images to 3D pre-operative images. If the patient is not
fixed during the intervention, the 2D image acquisition is
repeated several times during the procedure, and the
registration problem can be cast instead as a 3D tracking
problem. To solve the 3D problem, we propose in this paper
to apply 2D region tracking to first recover the components
of the transformation that are in-plane to the
projections. The 2D motion estimates of all projections are
backprojected into 3D space, where they are then combined
into a consistent estimate of the 3D motion. We compare this
method to intensity-based 2D-3D registration and a
combination of 2D motion backprojection followed by a 2D-3D
registration stage. Using clinical data with a fiducial
marker-based gold-standard transformation, we show that our
method is capable of accurately tracking vertebral targets
in 3D from 2D motion measured in x-ray projection
images. Using a standard tracking algorithm (hyperplane
tracking), tracking is achieved at video frame rates but
fails relatively often (32\% of all frames tracked with
target registration error (TRE) better than 1.2\,mm, 82\% of
all frames tracked with TRE better than 2.4\,mm). With
intensity-based 2D-2D image registration using normalized
mutual information (NMI) and pattern intensity (PI),
accuracy and robustness are substantially improved. NMI
tracked 82\% of all frames in our data with TRE better than
1.2\,mm and 96\% of all frames with TRE better than
2.4\,mm. This comes at the cost of a reduced frame rate,
1.7\,s average processing time per frame and projection
device. Results using PI were slightly more accurate, but
required on average 5.4\,s time per frame. These results are
still substantially faster than 2D-3D registration. We
conclude that motion backprojection from 2D motion tracking
is an accurate and efficient method for tracking 3D target
motion, but tracking 2D motion accurately and robustly
remains a challenge.},
keywords = {Real-time target tracking; 2D-3D registration; 2D-2D
registration; motion backprojection; frameless stereotactic
radiosurgery},
doi = {10.1109/TMI.2005.857651},
pdf = {2005-rohlfing-tmi-tracking_motion_backprojection.pdf},
category = {journal},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=32620&arnumber=1525181&count=11&index=5},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
pmid = {16279082}
}
@article{RohlMaur:2003,
author = {Rohlfing, Torsten and Maurer, Jr., Calvin R.},
title = {Nonrigid Image Registration in Shared-Memory Multiprocessor
Environments with Application to Brains, Breasts, and Bees},
pages = {16--25},
volume = 7,
number = 1,
year = 2003,
journal = {IEEE Transactions on Information Technology in Biomedicine},
abstract = {One major problem with nonrigid image registration
techniques is their high computational cost. Because of
this, these methods have found limited application to
clinical situations where fast execution is required, e.g.,
intra-operative imaging. This paper presents a parallel
implementation of a nonrigid image registration
algorithm. It takes advantage of shared-memory
multiprocessor computer architectures using multithreaded
programming by partitioning of data and partitioning of
tasks, depending on the computational subproblem. For three
different biomedical applications (intra-operative brain
deformation, contrast-enhanced MR mammography, inter-subject
brain registration), the scaling behavior of the algorithm
is quantitatively analyzed. The method is demonstrated to
perform the computation of intra-operative brain deformation
in less than a minute using 64 CPUs on a 128-CPU
shared-memory supercomputer (SGI Origin 3800). It is shown
that its serial component is no more than 2 percent of the
total computation time, allowing a speedup of at least a
factor of 50. In most cases, the theoretical limit of the
speedup is substantially higher (up to 132-fold in the
application examples presented in this paper). The parallel
implementation of our algorithm is therefore capable of
solving nonrigid registration problems with short execution
time requirements and may be considered an important step
in the application of such techniques to clinically
important problems such as the computation of brain
deformation during cranial image-guided surgery.},
keywords = {nonrigid image registration; high-performance computing;
multithreaded computations; parallel performance;
intra-operative brain deformation; contrast-enhanced MR
mammography; motion correction; inter-subject registration;
brain atlas},
pdf = {2003-rohlfing-titb-parallel_nonrigid.pdf},
pmid = {12670015},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isNumber=26609&prod=JNL&arnumber=1186522&arSt=+16&ared=+25&arAuthor=Rohlfing%2C+T.%3B+Maurer%2C+C.R.%2C+Jr.&arNumber=1186522&a_id0=1186520&a_id1=1186521&a_id2=1186522&a_id3=1186523&a_id4=1186524&a_id5=1186525&a_id6=1186526&a_id7=1186527&count=8},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
category = {journal}
}
@article{RohlMaur:2005,
author = {Rohlfing, Torsten and Maurer, Jr., Calvin R.},
title = {Multi-Classifier Framework for Atlas-Based Image
Segmentation},
journal = {Pattern Recognition Letters},
year = 2005,
volume = 26,
number = 13,
month = {Oct.},
pages = {2070--2079},
abstract = {Three different systematic approaches to generate multiple
classifiers in atlas-based biomedical image segmentation are
compared. Different atlases, as well as different
parametrization of the registration algorithm, lead to
different atlas-based classifiers. The classifier outputs
are combined and compared to a manual ground truth
segmentation. Classifier combination consistently improved
classification accuracy with the biggest improvement from
multiple atlases. We conclude that multi-classifier
techniques have a natural application to atlas-based
segmentation and increase classification accuracy in
real-world segmentation problems.},
keywords = {atlas-based segmentation; multiple classifier system;
bagging; nonrigid registration},
pdf = {2005-rohlfing-patrecoglet-multi_classifier_atlas_segmentation.pdf},
category = {journal},
doi = {10.1016/j.patrec.2005.03.017},
copyright = {Copyright for this paper is owned by Elsevier. The original
paper is available from sciencedirect.com.},
url = {http://www.sciencedirect.com/science/article/B6V15-4G2BFY3-B/2/f1b14350b5ef77078ec8c9bc44c9754f}
}
@article{RohlMaur:2007,
author = {Rohlfing, Torsten and Maurer, Jr., Calvin R.},
title = {Shape-Based Averaging},
journal = {IEEE Transactions on Image Processing},
year = 2007,
volume = 16,
number = 1,
pages = {153--161},
month = {Jan.},
abstract = {A new method for averaging multidimensional images is
presented, which is based on signed Euclidean distance maps
computed for each of the pixel values. We refer to the
algorithm as ``shape-based averaging'' (SBA) because of its
similarity to Raya and Udupa's shape-based interpolation
method. The new method does not introduce pixel intensities
that were not present in the input data, which makes it
suitable for averaging nonnumerical data such as label maps
(segmentations). Using segmented human brain magnetic
resonance images, SBA is compared to label voting for the
purpose of averaging image segmentations in a
multiclassifier fashion. SBA, on average, performed as well
as label voting in terms of recognition rates of the
averaged segmentations. SBA produced more regular and
contiguous structures with less fragmentation than did label
voting. SBA also was more robust for small numbers of
atlases and for low atlas resolutions, in particular, when
combined with shape-based interpolation. We conclude that
SBA improves the contiguity and accuracy of averaged image
segmentations.},
keywords = {Combination of segmentations; shape-based averaging (SBA);
shape-based interpolation (SBI); signed Euclidean distance
transform},
doi = {10.1109/TIP.2006.884936},
pdf = {2007-rohlfing-tip-shape_based_averaging.pdf},
pmid = {17283774},
url = {http://ieeexplore.ieee.org.laneproxy.stanford.edu/iel5/83/4032799/04032827.pdf?isnumber=4032799&prod=JNL&arnumber=4032827&arnumber=4032827&arSt=153&ared=161&arAuthor=Rohlfing%2C+T.%3B+Maurer%2C+Jr.%2C+C.+R.},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
category = {journal}
}
@article{RohlMaurBlue:2003,
author = {Rohlfing, Torsten and Maurer, Jr., Calvin R. and Bluemke,
David A. and Jacobs, Michael A.},
title = {Volume-Preserving Nonrigid Registration of {MR} Breast
Images Using Free-Form Deformation with an Incompressibility
Constraint},
journal = {IEEE Transactions on Medical Imaging},
year = 2003,
volume = 22,
number = 6,
pages = {730--741},
month = {Jun.},
abstract = {In this paper, we extend a previously reported
intensity-based non-rigid registration algorithm by using a
novel regularization term to constrain the
deformation. Global motion is modeled by a rigid
transformation while local motion is described by a
free-form deformation based on B-splines. An information
theoretic measure, normalized mutual information, is used as
an intensity-based image similarity measure. Registration is
performed by searching for the deformation that minimizes a
cost function consisting of a weighted combination of the
image similarity measure and a regularization term. The
novel regularization term is a local volume-preservation
(incompressibility) constraint, which is motivated by the
assumption that soft tissue is incompressible for small
deformations and short time periods. The incompressibility
constraint is implemented by penalizing deviations of the
Jacobian determinant of the deformation from unity. We apply
the non-rigid registration algorithm with and without the
incompressibility constraint to pre- and post-contrast MR
breast images from 17 patients. Without using a constraint,
the volume of contrast-enhancing lesions decreases by 1 to
78\% (mean 26\%). Image improvement (motion artifact
reduction) obtained using the new constraint is compared to
that obtained using a smoothness constraint based on the
bending energy of the coordinate grid by blinded visual
assessment of maximum intensity projections of subtraction
images. For both constraints, volume preservation improves,
and motion artifact correction worsens, as the weight of the
constraint penalty term increases. For a given volume change
of the contrast-enhancing lesions (2\% of the original
volume), the incompressibility constraint reduces motion
artifacts better than or equal to the smoothness constraint
in 13 out of 17 cases (better in 9, equal in 4, worse in
4). The preliminary results suggest that incorporation of
the incompressibility regularization term improves
intensity-based free-form non-rigid registration of
contrast-enhanced MR breast images by greatly reducing the
problem of shrinkage of contrast-enhancing structures while
simultaneously allowing motion artifacts to be substantially
reduced.},
keywords = {Non-rigid registration; free-form deformation; B-splines;
mutual information; volume preservation; contrast-enhanced
MR breast images},
doi = {10.1109/TMI.2003.814791},
pdf = {2003-rohlfing-tmi-constrained_deformation.pdf},
pmid = {12872948},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isNumber=27256&prod=JNL&arnumber=1211202&arSt=+730&ared=+741&arAuthor=Rohlfing%2C+T.%3B+Maurer%2C+C.R.%2C+Jr.%3B+Bluemke%2C+D.A.%3B+Jacobs%2C+M.A.&arNumber=1211202&a_id0=1211192&a_id1=1211195&a_id2=1211199&a_id3=1211201&a_id4=1211202&a_id5=1211203&a_id6=1211204&a_id7=1211205&a_id8=1211206&a_id9=1211207&a_id10=1211208&count=11},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
category = {journal}
}
@article{RohlMaurDean:2003,
author = {Rohlfing, Torsten and Maurer, Jr., Calvin R. and Dean, David
and Maciunas, Robert J.},
title = {Effect of changing patient position from supine to prone
on the accuracy of a {Brown-Roberts-Wells}
stereotactic head frame system},
journal = {Neurosurgery},
year = 2003,
volume = 52,
number = 3,
pages = {610--618},
month = {Mar.},
abstract = {OBJECTIVE: Despite the growing popularity of frameless
image-guided surgery systems, stereotactic frame systems are
widely accepted by neurosurgeons and are commonly used to
perform biopsies, functional procedures, and stereotactic
radiosurgery. We investigated the accuracy of the
Brown-Roberts-Wells stereotactic frame system when the
mechanical load on the frame changes between preoperative
imaging and the intervention because of different patient
position: supine during imaging, prone during intervention.
METHODS: We analyzed computed tomographic images acquired
from 14 patients who underwent stereotactic biopsy, deep
brain stimulator implantation, or radiosurgery. Two images
were acquired for each patient, one with the patient in the
supine position and one in the prone position. The prone
images were registered to the respective supine images by
use of an intensity-based registration algorithm, once using
only the frame and once using only the head. The difference
between the transformations produced by these two
registrations describes the movement of the patient's head
with respect to the frame.
RESULTS: The maximum frame-based registration error between
the supine and prone positions was 2.8 mm; it was more than
2 mm in two patients and more than 1.5 mm in six
patients. Anteroposterior translation is the dominant
component of the difference transformation for most
patients. In general, the magnitude of the movement
increased with brain volume, which is an index of head
weight.
CONCLUSION: To minimize frame-based registration error
caused by a change in the mechanical load on the frame,
stereotactic procedures should be performed with the patient
in the identical position during imaging and intervention.},
keywords = {Image-guided surgery; Mechanical stress; Prone position;
Stereotactic head frame system; Stereotactive radiosurgery;
Stereotactic techniques; Stereotaxy; Supine position},
pdf = {2003-rohlfing-neurosurgery-frame_supine_prone.pdf},
copyright = {Copyright for this paper is owned by the Congress of
Neurological Surgeons. The original paper is avaliable from
www.neurosurgery-online.com},
pmid = {12590686},
url = {http://www.neurosurgery-online.com/abstracts/5203/NURO52030610_abs.html},
category = {journal}
}
@article{RohlMaurODel:2004,
author = {Rohlfing, Torsten and Maurer, Jr., Calvin R. and O'Dell,
Walter G. and Zhong, Jianhui},
title = {Modeling Liver Motion and Deformation During the Respiratory
Cycle Using Intensity-Based Free-Form Registration of Gated
{MR} Images},
journal = {Medical Physics},
year = 2004,
volume = 31,
number = 3,
pages = {427--432},
month = {Mar.},
abstract = {We present a technique for modeling liver motion during the
respiratory cycle using intensity-based non-rigid
registration of gated magnetic resonance (MR)
images. Three-dimensional MR images of the abdomens of four
volunteers were acquired at end-inspiration, end-expiration,
and eight time points in between using respiratory
gating. The deformation fields between the images were
computed using intensity-based rigid and non-rigid
registration algorithms. Global motion is modeled by a rigid
transformation while local motion is modeled by a free-form
deformation based on B-splines. Much of the liver motion was
cranial-caudal translation, and thus the rigid
transformation captured much of the motion. However, there
was still substantial residual deformation (approximately
10mm averaged over the entire liver in four volunteers,
and 34mm at one place in the liver of one volunteer). The
computed organ motion model can potentially be used to
determine an appropriate respiratory-gated radiotherapy
window during which the position of the target is known
within a specified excursion.},
keywords = {non-rigid image registration; free-form spline-based
deformation; liver motion; respiration-gated MR images},
doi = {10.1118/1.1644513},
pdf = {2004-rohlfing-medphys-liver_motion_modeling.pdf},
url = {http://link.aip.org/link/?MPH/31/427/1},
category = {journal},
copyright = {Copyright for this paper is owned by the American
Association of Physicists in Medicine. The original paper is
available at www.medphys.org.},
pmid = {15070239}
}
@article{RohlRussDenz:2005,
author = {Rohlfing, Torsten and Russakoff, Daniel B. and Denzler,
Joachim and Mori, Kensaku and Maurer, Jr., Calvin R.},
title = {Progressive attenuation fields: Fast {2D}-{3D} registration
without precomputation},
journal = {Medical Physics},
year = 2005,
volume = 32,
number = 9,
pages = {2870--2880},
month = {Sep.},
abstract = {Computation of digitally reconstructed radiograph (DRR)
images is the rate-limiting step in most current
intensity-based algorithms for the registration of
three-dimensional (3D) images to two-dimensional (2D)
projection images. This paper introduces and evaluates the
progressive attenuation field (PAF), which is a new method
to speed up DRR computation. A PAF is closely related to an
attenuation field (AF). A major difference is that a PAF is
constructed on the fly as the registration proceeds; it does
not require any precomputation time, nor does it make any
prior assumptions of the patient pose or limit the
permissible range of patient motion. A PAF effectively acts
as a cache memory for projection values once they are
computed, rather than as a lookup table for precomputed
projections like standard AFs. We use a cylindrical
attenuation field parameterization, which is better suited
for many medical applications of 2D-3D registration than the
usual two-plane parameterization. The computed attenuation
values are stored in a hash table for time-efficient storage
and access. Using clinical gold-standard spine image data
sets from five patients, we demonstrate consistent speedups
of intensity-based 2D-3D image registration using PAF DRRs
by a factor of ten over conventional ray casting DRRs with
no decrease of registration accuracy or robustness.},
keywords = {2D-3D Image Registration; Digitally Reconstructed
Radiograph; DRR; Attenuation Field; Precomputation;
Computational Performance},
doi = {10.1118/1.1997367},
pdf = {2005-rohlfing-medphys-progressive_attenuation_fields.pdf},
url = {http://link.aip.org/link/?MPH/32/2870/1},
pmid = {16266101},
category = {journal}
}
@article{RohlRussMaur:2004,
author = {Rohlfing, Torsten and Russakoff, Daniel B. and Maurer, Jr.,
Calvin R.},
title = {Performance-Based Classifier Combination in Atlas-Based
Image Segmentation Using Expectation-Maximization Parameter
Estimation},
journal = {IEEE Transactions on Medical Imaging},
volume = 23,
number = 8,
month = {Aug.},
year = 2004,
category = {journal},
pages = {983--994},
abstract = {It is well known in the pattern recognition community that
the accuracy of classifications obtained by combining
decisions made by independent classifiers can be
substantially higher than the accuracy of the individual
classifiers. We have previously shown this to be true for
atlas-based segmentation of biomedical images. The
conventional method for combining individual classifiers
weights each classifier equally (vote or sum rule
fusion). In this paper, we propose two methods that estimate
the performances of the individual classifiers and combine
the individual classifiers by weighting them according to
their estimated performance. The two methods are multiclass
extensions of an expectation-maximization (EM) algorithm for
ground truth estimation of binary classification based on
decisions of multiple experts (Warfield , 2004). The first
method performs parameter estimation independently for each
class with a subsequent integration step. The second method
considers all classes simultaneously. We demonstrate the
efficacy of these performance-based fusion methods by
applying them to atlas-based segmentations of
three-dimensional confocal microscopy images of bee
brains. In atlas-based image segmentation, multiple
classifiers arise naturally by applying different
registration methods to the same atlas, or the same
registration method to different atlases, or both. We
perform a validation study designed to quantify the success
of classifier combination methods in atlas-based
segmentation. By applying random deformations, a given
ground truth atlas is transformed into multiple
segmentations that could result from imperfect registrations
of an image to multiple atlas images. In a second evaluation
study, multiple actual atlas-based segmentations are
combined and their accuracies computed by comparing them to
a manual segmentation. We demonstrate in both evaluation
studies that segmentations produced by combining multiple
individual registration-based segmentations are more
accurate for the two classifier fusion methods we propose,
which weight the individual classifiers according to their
EM-based performance estimates, than for simple sum rule
fusion, which weights each classifier equally.},
keywords = {Atlas-based segmentation; classifier performance;
expectation-maximization (EM) parameter estimation; mixture
of experts; multiclassifier decision fusion},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isNumber=29222&prod=JNL&arnumber=1318724&arSt=+983&ared=+994&arAuthor=+Rohlfing%2C+T.%3B++Russakoff%2C+D.B.%3B++Maurer%2C+C.R.%2C+Jr.&arNumber=1318724&a_id0=1318716&a_id1=1318717&a_id2=1318718&a_id3=1318719&a_id4=1318720&a_id5=1318721&a_id6=1318722&a_id7=1318723&a_id8=1318724&a_id9=1318725&a_id10=1318726&a_id11=1318727&a_id12=1318728&a_id13=1318729&a_id14=1318730&count=15},
doi = {10.1109/TMI.2004.830803},
pdf = {2004-rohlfing-tmi-multi_classifier_performance.pdf},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
pmid = {15338732}
}
@article{RohlSchaHadd:2005,
author = {Rohlfing, Torsten and Schaupp, Frank and Haddad, Daniel and
Brandt, Robert and Haase, Axel and Menzel, Randolf and
Maurer, Jr., Calvin R.},
title = {Unwarping Confocal Microscopy Images of Bee Brains by
Nonrigid Registration to a Magnetic Resonance Microscopy
Image},
journal = {Journal of Biomedical Optics},
year = 2005,
volume = 10,
number = 2,
month = {Mar.},
eid = {024018},
numpages = {8},
pages = {024018},
abstract = {Confocal microscopy (CM) is a powerful image acquisition
technique that is well established in many biological
applications. It provides three-dimensional acquisition with
high spatial resolution and can acquire several different
channels of complementary image information. Due to the
specimen extraction and preparation process, however, the
shapes of imaged objects may differ considerably from their
in vivo appearance. Magnetic resonance microscopy (MRM) is
an evolving variant of magnetic resonance imaging, which
achieves microscopic resolutions using a high magnetic field
and strong magnetic gradients. Compared to CM imaging, MRM
allows for in situ imaging and is virtually free of
geometrical distortions. We propose in this paper to combine
the advantages of both methods by unwarping CM images using
a MRM reference image. Our method incorporates a sequence of
image processing operators applied to the MRM image,
followed by a two-stage intensity-based registration to
compute a nonrigid coordinate transformation between the CM
images and the MRM image. We present results obtained using
CM images from the brains of 20 honey bees and a MRM image
of an in situ bee brain.},
keywords = {Confocal microscopy imaging; magnetic resonance microscopy;
nonrigid image registration; geometrical distortion},
category = {journal},
url = {http://link.aip.org/link/?JBO/10/024018/1},
doi = {10.1117/1.1896025},
pdf = {2005-rohlfing-jbo-unwarp_cm_to_mrm.pdf},
pmid = {15910092}
}
@article{RohlSullPfef:2006,
author = {Rohlfing, Torsten and Sullivan, Edith V. and Pfefferbaum,
Adolf},
title = {Deformation-Based Brain Morphometry to Track the Course of
Alcoholism: Differences between Intra-Subject and
Inter-Subject Analysis},
journal = {Psychiatry Research: Neuroimaging},
year = 2006,
volume = 146,
number = 2,
pages = {157--170},
month = {Feb.},
abstract = {Substantial changes in brain morphology mark the course of
alcoholism from development through dependence, recovery,
and relapse. These changes can be characterized with
deformation-based morphometry, which quantifies shape
differences between anatomical structures, either in
different subjects (cross-sectional) or in the same subject
over time (longitudinal). Here we present analyses of image
data from a longitudinal MRI study on the effects of
alcoholism on brain structure. Images were acquired from
alcoholic women ($n=7$, mean age 47.8 $\pm$ 8.3 years) and
age-matched control women ($n=16$, mean age 51.2 $\pm$ 7.5
years). From each subject, we acquired two structural MR
brain images, separated by approximately two years (mean
21.6 $\pm$ 7 months). We performed two types of morphometry
using log-Jacobian maps of inter-subject and intra-subject
nonrigid coordinate transformations, justified by the
invariance of relevant statistics (mean, standard deviation,
z-score, and t-test) under changes of the spatial and
temporal reference coordinate system. With all images from
one time point, a cross-sectional inter-subject morphometry
determined group differences between alcoholics and normal
controls. We compared these results with longitudinal
intra-subject morphometry based on two images per subject
acquired at different times (approximately two years
apart). Inter- and intra-subject analysis produced partially
conflicting results. Whereas the intra-subject analysis
indicated faster ventricular volume increases in the
alcoholics (+11\% per year) than in the controls (+2\% per
year), the inter-subject analysis showed, on average,
smaller absolute ventricle volumes in the alcoholics than in
the controls (-33\% relative volume). These differences
were confirmed by manual planimetry and were statistically
significant whether tested based on difference or change,
integrated over the volume of the ventricles. Other changes
and group differences were consistent between the two
analyses, e.g., reduction of white matter (including corpus
callosum) and increase in CSF volume, and these are in
agreement with established effects of alcoholism on brain
structure. We conclude that intra-subject morphometry of
longitudinal data is preferable to inter-subject morphometry
for detecting dynamic changes due to a disease, especially
when only small samples are available. Our analysis
demonstrates that the distinction between group differences
observed at a point in time vs. over time is not merely
academic but can substantially reduce the validity of the
outcomes of actual morphometric studies. This discrepancy in
results underscores the importance of distinguishing between
volume differences and volume changes in morphometric
analyses.},
keywords = {Deformation-based morphometry; Magnetic resonance images;
Longitudinal analysis; Cross-sectional analysis;
Alcoholism},
doi = {10.1016/j.pscychresns.2005.12.002},
pdf = {2006-rohlfing-psyn-dbm_alcoholism_inter_vs_intra_subject.pdf},
pmid = {16500088},
category = {journal},
url = {http://www.sciencedirect.com/science/article/B6TBW-4JB9MTN-2/2/cec3fe40325cdd8a213a2fb6c9390169}
}
@article{RohlWestBeie:2000,
author = {Rohlfing, Torsten and West, Jay B. and Beier, J\"urgen and
Liebig, Thomas and Taschner, Christian A. and Thomale,
Ulrich-Wilhelm },
title = {Registration of Functional and Anatomical {MRI}: Accuracy
Assessment and Application in Navigated Neurosurgery},
journal = {Computer Aided Surgery},
year = 2000,
volume = 5,
number = 6,
pages = {414--425},
abstract = {OBJECTIVE: A procedure for acquisition, automated
registration, and fusion of functional and anatomical
magnetic resonance images is presented. Its accuracy is
quantitatively assessed using a publicly available gold
standard. A patient case is used to illustrate the
technique's clinical usefulness in image-guided
neurosurgery.
MATERIALS AND METHODS: Before and after functional MRI
(fMRI) acquisition, additional anatomical images were
acquired at spatial locations identical to those of the
functional images (5-10 slices) for the purpose of
voxel-based image registration. Registration accuracy of the
anatomical volumes and high-resolution 3D MRI volumes
(MP-RAGE imaging) was quantified using adapted data (8
patients) originating from the Vanderbilt Retrospective
Registration Evaluation Project (NIH project 1 R01
NS33926-02). Selecting three subsets of slices from that
data (5 slices/6 mm slice distance, 10 slices/3 mm distance,
and 10 slices/6 mm distance), the small number of images
available from fMRI acquisition was taken into
account. Accuracies in registering these sparse data sets
were then compared to the accuracy achieved using complete
data. For clinical patient data (16 patients), fMRI images
were fused with MP-RAGE images, thereby integrating
anatomical images with information about the locations of
functional areas. The resulting images were used for
planning and navigation during tumor resections using an
operating microscope (MKM, Zeiss).
RESULTS: Quantitative analysis showed no loss of
registration accuracy due to a reduced number of slices,
regardless of whether 5 or 10 slices were used. For
small-volume coverage in the anatomical images (thickness 24
mm), registration of one patient failed, and this could
easily be identified by visual inspection. No failures were
experienced when 54 mm was covered. In the clinical
environment, all 16 interventions using fused fMRI and MRI
data were successful.
CONCLUSIONS: Automatic registration of functional and
high-resolution anatomical MRI was found to be sufficiently
accurate and reliable for use in stereotactic
neurosurgery.},
keywords = {functional MRI; MP-RAGE; registration accuracy; image
fusion},
issn = {1092-9088},
pdf = {2000-rohlfing-cas-fmri_registration.pdf},
pmid = {11295854},
doi = {10.1002/igs.1003},
copyright = {Copyright for this article is owned by Wiley-Liss, Inc. The
original paper is available from www.interscience.wiley.com},
url = {http://www3.interscience.wiley.com/cgi-bin/abstract/77005128/ABSTRACT},
category = {journal}
}
@article{RoseRohlORei:2007,
author = {Rosenbloom, Margaret J. and Rohlfing, Torsten and O'Reilly,
Anne W. and Sassoon, Stephanie A. and Pfefferbaum, Adolf and
Sullivan, Edith V.},
title = {Improvement in Memory and Static Balance with Abstinence in
Alcoholic Men and Women: Selective Relations with Changes in
Regional Ventricular Volumes},
journal = {Psychiatry Research: Neuroimaging},
year = 2007,
category = {journal},
volume = 155,
number = 2,
pages = {91--102},
month = {Jul.},
abstract = {We investigated whether changes in memory or static balance
in chronic alcoholics, occurring with abstinence or relapse,
are associated with changes in lateral and fourth
ventricular volume. Alcoholics meeting DSM-IV criteria for
Alcohol Dependence (n = 15) and non-alcoholic controls (n =
26) were examined twice at a mean interval of 2 years with
standard Wechsler Abbreviated Scale of Intelligence (WASI),
Wechsler Memory Scale~Revised (WMS-R) tests, an ataxia
battery, and structural MRI. At study entry, alcoholics had
been abstinent on average for over 4 months and achieved
lower scores than controls on WASI General IQ Index, WMS-R
General Memory Index, and the ataxia battery. The 10
alcoholics who maintained sobriety at retest did not differ
at study entry in socio-demographic measures, alcohol use,
or WASI and WMS-R summary scores from the five relapsers. At
follow-up, abstainers improved more than controls on the
WMS-R General Memory Index. Ataxia tended to improve in
abstainers relative to controls. Associations were observed
between memory and lateral ventricular volume change and
between ataxia and fourth ventricular volume change in
alcoholics but not in the controls. Both memory and ataxia
can improve with sustained sobriety, and brain~behavior
associations suggest selective brain structural substrates
for the changes observed.},
keywords = {MRI; Ventricles; Recovery; Ataxia; Brain~behavior
association},
doi = {10.1016/j.pscychresns.2006.12.019},
url = {http://www.sciencedirect.com/science/article/B6TBW-4NDDSYT-1/2/f75aaf2020919052bbf2af8030880afa},
pdf = {2007-rosenbloom-psyn-improvement_memory_balance_abstinence.pdf},
pmid = {17407808},
pmc = {1949491},
category = {journal}
}
@article{RufLopeStei:2004,
author = {Ruf, Juri and Lopez H\"a{}nninen, E. and Steinm\"u{}ller, T.
and Rohlfing, Torsten and Bertram, Helga and Gutberlet,
Matthias and Lemke, Arne-J\"o{}rn and Felix, Roland and
Amthauer, Holger},
title = {Preoperative localization of parathyroid glands -- Use of
{MRI}, scintigraphy, and image fusion},
journal = {Nuklearmedizin},
year = 2004,
volume = 43,
number = 3,
pages = {85--90},
month = {Jun.},
abstract = {AIM: Minimally invasive resection of hyperfunctional
parathyroid glands is an alternative to open
surgery. However, it requires a precise preoperative
localization. This study evaluated the diagnostic use of
magnetic resonance (MR) imaging, parathyroid scintigraphy,
and consecutive image fusion. PATIENTS, METHODS: 17 patients
(9 women, 8 men; age: 29-72 years; mean: 51.2 years) with
primary hyperparathyroidism were included. Examination by
MRI used unenhanced T1- and T2-weighted sequences as well as
contrast-enhanced T1-weighted sequences. (99m)Tc-MIBI
scintigraphy consisted of planar and SPECT (single photon
emission tomography) imaging techniques. In order to improve
the anatomical localization of a scintigraphic focus,
SPECT-data were fused with the corresponding MR-data using a
modified version of the Express 5.0 software (Advanced
Visual Systems, Waltham, MA). Results of image fusion were
then compared to histopathology. RESULTS: In 14/17 patients,
a single parathyroid adenoma was found. There were 3 cases
with hyperplastic glands. MRI detected 10 (71\%),
scintigraphy 12 (86\%) adenomas. Both modalities detected
1/3 patients with hyperplasia. Image fusion improved the
anatomical assignment of the 13 scintigraphic foci in five
patients and was helpful in the interpretation of
inconclusive MR-findings in two patients. CONCLUSIONS: Both
MRI and (99m)Tc-MIBI scintigraphy sensitively detect
parathyroid adenomas but are less reliable in case of
hyperplastic glands. In case of a scintigraphic focus, image
fusion considerably improves its topographic
assignment. Furthermore, it facilitates the evaluation of
inconclusive MRI findings.},
keywords = {Parathyroid gland, adenoma, scintigraphy, magnetic resonance
imaging, image fusion},
url = {http://www.schattauer.de/zs/nukl/artikel.asp?path=/zs/nukl/2004/3/&nummer=nu04030085},
pdf = {2004-ruf-nuklearmedizin-preoperative_localization_parathyroid_glands.pdf},
category = {journal},
pmid = {15201949}
}
@article{RussRohlAdle:2005,
author = {Russakoff, Daniel B. and Rohlfing, Torsten and Adler, Jr.,
John R. and Maurer, Jr., Calvin R.},
title = {Intensity-Based {2D}-{3D} Spine Image Registration
Incorporating a Single Fiducial Marker},
journal = {Academic Radiology},
year = 2005,
volume = {12},
number = {1},
month = {Jan.},
pages = {37--50},
abstract = {RATIONALE AND OBJECTIVES. The 2D-3D registration of a CT
image to one or more x-ray projection images has a number
of image-guided therapy applications. Fiducial marker-based
methods are in general fast, accurate, and robust, but
marker implantation is not always possible, is often
considered too invasive to be clinically acceptable, and
entails risk. There is also the unresolved issue of whether
it is acceptable to leave markers permanently
implanted. Intensity-based registration methods do not
require the use of markers and can be automated because
geometric features such as points and surfaces do not need
to be segmented from the images. For spine images, however,
intensity-based methods are susceptible to local optima in
the cost function and thus need initial transformations that
are close to the correct transformation.
MATERIALS AND METHODS. In this paper, we propose a hybrid
similarity measure for 2D-3D registration that is a weighted
combination of an intensity-based similarity measure (mutual
information) and a point-based measure using one fiducial
marker. We evaluate its registration accuracy and robustness
using gold-standard clinical spine image data from four
patients.
RESULTS. The mean registration error for successful
registrations over the four patients was 1.3 and 1.1 mm for
the intensity-based and hybrid similarity measures,
respectively. Whereas the percentage of successful
intensity-based registrations (registration error less than
2.5 mm) decreased rapidly as the initial transformation got
further from the correct transformation, the incorporation
of a single marker produced successful registrations more
than 99\% of the time independent of the initial
transformation.
CONCLUSION. The use of one fiducial marker reduces 2D-3D
spine image registration error slightly and improves
robustness substantially. The findings are potentially
relevant for image-guided therapy. If one marker is
sufficient to obtain clinically acceptable registration
accuracy and robustness, as the preliminary results using
the proposed hybrid similarity measure suggest, the marker
can be placed on a spinous process, which could be
accomplished without penetrating muscle or using
fluoroscopic guidance, and such a marker could be removed
relatively easily.},
keywords = {2D-3D image registration; fiducial marker; image-guided
surgery; radiosurgery},
pdf = {2005-russakoff-acadradiol-single_marker_registration_2d_3d.pdf},
category = {journal},
doi = {10.1016/j.acra.2004.09.013},
url = {http://www.sciencedirect.com/science/article/B75BK-4DXT7V8-1/2/6ba7444c9eaba3504b3896cc0303b172},
copyright = {Copyright for this paper is owned by Elsevier. The original
paper is available from sciencedirect.com.},
pmid = {15691724}
}
@article{RussRohlMori:2005,
author = {Russakoff, Daniel B. and Rohlfing, Torsten and Mori, Kensaku
and Rueckert, Daniel and Adler, Jr., John R. and Maurer,
Jr., Calvin R.},
title = {Fast generation of digitally reconstructed radiographs using
attenuation fields with application to {2D}-{3D} image
registration},
journal = {IEEE Transactions on Medical Imaging},
year = 2005,
volume = 24,
number = 11,
pages = {1441--1454},
month = {Nov.},
abstract = {Generation of digitally reconstructed radiographs (DRRs) is
computationally expensive and is typically the rate-limiting
step in the execution time of intensity-based 2D-3D
registration algorithms. We address this computational
issue by extending the technique of light field rendering
from the computer graphics community. The extension of
light fields, which we call attenuation fields (AFs), allows
most of the DRR computation to be performed in a
preprocessing step; after this precomputation step, DRRs can
be generated substantially faster than with conventional ray
casting. We derive expressions for the physical sizes of
the two planes of an AF necessary to generate DRRs for a
given X-ray camera geometry and all possible object motion
within a specified range. An AF can require substantial
memory, which we address by compressing it using vector
quantization. We compare DRRs generated using AFs (AF-DRRs)
to those generated using ray casting (RC-DRRs) for a typical
C-arm geometry and CT images of several anatomic regions.
They are quantitatively very similar: the median peak
signal-to-noise ratio of AF-DRRs vs.\ RC-DRRs is greater
than 43\,dB in all cases. We perform intensity-based 2D-3D
registration using AF-DRRs and RC-DRRs and evaluate
registration accuracy using gold-standard clinical spine
image data from four patients. The registration accuracy
and robustness of the two methods is virtually identical
whereas the execution speed using AF-DRRs is an order of
magnitude faster.},
keywords = {Digitally reconstructed radiographs; light fields;
intensity-based 2D-3D image registration; image-guided
therapy},
doi = {10.1109/TMI.2005.856749},
pdf = {2005-russakoff-tmi-attenuation_fields.pdf},
category = {journal},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=32620&arnumber=1525180&count=11&index=4},
copyright = {Copyright to this article is owned by the IEEE. The
original publication is available at ieeexplore.ieee.org},
pmid = {16279081}
}
@article{SullRoseRohl:2009,
author = {Sullivan, Edith V. and Rose, Jessica and Rohlfing, Torsten
and Pfefferbaum, Adolf},
title = {Postural sway reduction in aging men and women: Relation to
brain structure, cognitive status, and stabilizing factors},
journal = {Neurobiology of Aging},
year = 2009,
volume = 30,
number = 5,
pages = {793--807},
month = {May},
abstract = {Postural stability becomes compromised with advancing age,
but the neural mechanisms contributing to instability have
not been fully explicated. Accordingly, this quantitative
physiological and MRI study of sex differences across the
adult age range examined the association between components
of postural control and the integrity of brain structure and
function under different conditions of sensory input and
stance stabilization manipulation. The groups comprised 28
healthy men (age 30-73 years) and 38 healthy women (age
34-74 years), who completed balance platform testing,
cognitive assessment, and structural MRI. The results
supported the hypothesis that excessive postural sway would
be greater in older than younger healthy individuals when
standing without sensory or stance aids, and that
introduction of such aids would reduce sway in both
principal directions (anterior-posterior and medial-lateral)
and in both the open-loop and closed-loop components of
postural control even in older individuals. Sway reduction
with stance stabilization, that is, standing with feet
apart, was greater in men than women, probably because older
men were less stable than women when standing with their
feet together. Greater sway was related to evidence for
greater brain structural involutional changes, indexed as
ventricular and sulcal enlargement and white matter
hyperintensity burden. In women, poorer cognitive test
performance related to less sway reduction with the use of
sensory aids. Thus, aging men and women were shown to have
diminished postural control, associated with cognitive and
brain structural involution, in unstable stance conditions
and with diminished sensory input.},
keywords = {Postural control; Posturography; Balance; Cerebellum; Brain;
MRI; White matter hyperintensity; Sway; Age; Sex},
doi = {10.1016/j.neurobiolaging.2007.08.021},
pdf = {2009-sullivan-nba-postural_sway_reduction.pdf},
pmid = 17920729,
category = {journal}
}