Free-Form B-spline Deformation Model for Groupwise Registration

In this work, we extend a previously demonstrated entropy based groupwise registration method to include a free-form deformation model based on B-splines. We provide an efficient implementation using stochastic gradient descents in a multi-resolution setting. We demonstrate the method in application to a set of 50 MRI brain scans and compare the results to a pairwise approach using segmentation labels to evaluate the quality of alignment. Our results indicate that increasing the complexity of the deformation model improves registration accuracy significantly, especially at cortical regions

Non-rigid Groupwise Registration using B-Spline Deformation Model -- Release 0.00

In this work, we extend a previously demonstrated entropy based groupwise registration method to include a non-rigid deformation model based on B-splines. We describe an open source implementation of the groupwise registration algorithm using the Insight Toolkit ITK www.itk.org. We provide the source code, parameters, input and output data that we used for validation. We describe an efficient implementation of the algorithm by using a stochastic optimization scheme embedded in a multi-resolution setting. The objective function is optimized using gradient descent algorithm combined with line search for the step size. The derivative of the objective function is evaluated efficiently by computing Jacobian of B-spline deformation field locally. We demonstrate the algorithm in application to different imaging modalities including proton density, FA, T1 and T2 MR images. We validate the algorithm on synthetic datasets varying from 2 to 30 images b

Image-Driven Population Analysis Through Mixture Modeling

We present iCluster, a fast and efficient algorithm that clusters a set of images while co-registering them using a parameterized, nonlinear transformation model. The output of the algorithm is a small number of template images that represent different modes in a population. This is in contrast with traditional, hypothesis-driven computational anatomy approaches that assume a single template to construct an atlas. We derive the algorithm based on a generative model of an image population as a mixture of deformable template images. We validate and explore our method in four experiments. In the first experiment, we use synthetic data to explore the behavior of the algorithm and inform a design choice on parameter settings. In the second experiment, we demonstrate the utility of having multiple atlases for the application of localizing temporal lobe brain structures in a pool of subjects that contains healthy controls and schizophrenia patients. Next, we employ iCluster to partition a data set of 415 whole brain MR volumes of subjects aged 18 through 96 years into three anatomical subgroups. Our analysis suggests that these subgroups mainly correspond to age groups. The templates reveal significant structural differences across these age groups that confirm previous findings in aging research. In the final experiment, we run iCluster on a group of 15 patients with dementia and 15 age-matched healthy controls. The algorithm produces two modes, one of which contains dementia patients only. These results suggest that the algorithm can be used to discover subpopulations that correspond to interesting structural or functional “modes.”National Science Foundation (CAREER Grant 0642971)National Institute of Mental Health Grant (5R01-MH050740-13)Morphometry Biomedical Informatics Research Network (NIH NCRR mBIRN U24-RR021382) and (NIH NINDS R01-NS051826 grant)Neuroimaging Analysis Center (NIH CRR NAC P41-RR13218)National Alliance for Medical Image Analysis (NIH NIBIB NAMIC U54-ED005149)Dept. of Veterans Affairs Merit Award

Reappraisal of T1b gallbladder cancer (GBC): clinicopathologic analysis of 473 in situ and invasive GBCs and critical review of the literature highlights its rarity, and that it has a very good prognosis

There are highly conflicting data on relative frequency (2–32%), prognosis, and management of pT1b-gallbladder carcinoma (GBC), with 5-year survival ranging from > 90% in East/Chile where cholecystectomy is regarded as curative, versus 90%, similar to findings in the East. This supports the inclusion of pT1b in the “early GBC” category, as is typically done in high-incidence regions. Pathologic mis-staging of pT2 as pT1 is not uncommon. Cases should not be classified as pT1b unless extensive, preferably total, sampling of the gallbladder to rule out a subtle pT2 is performed. Critical appraisal of the literature reveals that the Western guidelines are based on either SEER or mis-interpretation of stage IB cases as “pT1b.” Although the prognosis of pT1b-GBC is very good, additional surgery (radical cholecystectomy) may be indicated, and long-term surveillance of the biliary tract is warranted

Hepatic Cysts Reappraisal of the Classification, Terminology, Differential Diagnosis, and Clinicopathologic Characteristics in 258 Cases

The literature on liver cysts is highly conflicting, mostly owing to definitional variations. Two hundred and fifty-eight >= 1 cm cysts evaluated pathologically using updated criteria were classifiable as: I. Ductal plate malformation related (63%); that is, cystic bile duct hamartoma or not otherwise specified-type benign biliary cyst (35 with polycystic liver disease). These were female predominant (F/M=2.4), large (10 cm), often multifocal with degenerative/inflammatory changes and frequently misclassified as "hepatobiliary cystadenoma." II. Neoplastic (13%); 27 (10.5%) had ovarian-type stroma (OTS) and qualified as mucinous cystic neoplasm (MCN) per World Health Organization (WHO). These were female, solitary, mean age 52, mean size 11 cm, and 2 were associated with carcinoma (1 in situ and 1 microinvasive). There were 3 intraductal papillary neoplasms, 1 intraductal oncocytic papillary neoplasm, 1 cystic cholangiocarcinoma, and 2 cystic metastasis. III. Infectious/inflammatory (12%). These included 23 hydatid cysts (including 2 Echinococcus alveolaris both misdiagnosed preoperatively as cancer), nonspecific inflammatory cysts (abscesses, inflammatory cysts: 3.4%). IV. Congenital (7%). Mostly small (<3 cm); choledochal cyst (5%), foregut cyst (2%). V. Miscellaneous (4%). In conclusion, hepatic cysts occur predominantly in women (3/1), are mostly (90%) non-neoplastic, and seldom (<2%) malignant. Cystic bile duct hamartomas and their relative not otherwise specified-type benign biliary cysts are frequently multifocal and often misdiagnosed as "cystadenoma/carcinoma." Defined by OTS, MCNs (the true "hepatobiliary cystadenoma/carcinoma") are solitary, constitute only 10.5% of hepatic cysts, and have a significantly different profile than the impression in the literature in that essentially all are perimenopausal females, and rarely associated with carcinoma (7%). Since MCNs can only be diagnosed by demonstration of OTS through complete microscopic examination, it is advisable to avoid the term "cystadenoma/cystadenocarcinoma" solely based on radiologic examination, and the following simplified terminology would be preferable in preoperative evaluation to avoid conflicts with the final pathologic diagnosis: (1) noncomplex (favor benign), (2) complex (in 3 subsets, as favor benign, cannot rule out malignancy, or favor malignancy), (3) malignant features

Substaging Nodal Status in Ampullary Carcinomas has Significant Prognostic Value: Proposed Revised Staging Based on an Analysis of 313 Well-Characterized Cases

Current nodal staging (N-staging) of ampullary carcinoma in the TNM staging system distinguishes between node-negative (N0) and node-positive (N1) disease but does not consider the metastatic lymph node (LN) number

T2 gallbladder cancer shows substantial survival variation between continents and this is not due to histopathologic criteria or pathologic sampling differences

Published data on survival of T2 gallbladder carcinoma (GBC) from different countries show a wide range of 5-year survival rates from 30-> 70%. Recently, studies have demonstrated substantial variation between countries in terms of their approach to sampling gallbladders, and furthermore, that pathologists from different continents apply highly variable criteria in determining stage of invasion in this organ. These findings raised the question of whether these variations in pathologic evaluation could account for the vastly different survival rates of T2 GBC reported in the literature. In this study, survival of 316 GBCs from three countries (Chile n = 137, South Korea n = 105, USA n = 74), all adequately sampled (with a minimum of five tumor sections examined) and histopathologically verified as pT2 (after consensus examination by expert pathologists from three continents), was analyzed. Chilean patients had a significantly worse prognosis based on 5-year all-cause mortality (HR: 1.89, 95% CI: 1.27-2.83, p = 0.002) and disease-specific mortality (HR: 2.41, 95% CI: 1.51-3.84, p < 0.001), compared to their South Korean counterparts, even when controlled for age and sex. Comparing the USA to South Korea, the survival differences in all-cause mortality (HR: 1.75, 95% CI: 1.12-2.75, p = 0.015) and disease-specific mortality (HR: 1.94, 95% CI: 1.14-3.31, p = 0.015) were also pronounced. The 3-year disease-specific survival rates in South Korea, the USA, and Chile were 75%, 65%, and 55%, respectively, the 5-year disease-specific survival rates were 60%, 50%, and 50%, respectively, and the overall 5-year survival rates were 55%, 45%, and 35%, respectively. In conclusion, the survival of true T2 GBC in properly classified cases is neither as good nor as bad as previously documented in the literature and shows notable geographic differences even in well-sampled cases with consensus histopathologic criteria. Future studies should focus on other potential reasons including biologic, etiopathogenetic, management-related, populational, or healthcare practice-related factors that may influence the survival differences of T2 GBC in different regions