\nocite{*} ######################################################################################## # Instructions for updating citation list # # Input one keyword (including ’Slicer Tractography’, ‘Slicer DTI’ and ‘SlicerDMI’) into GoogleScholar, and limit the search according to the publication years (e.g. since 2017). # # For each searched paper, there is a brief introduction under the title. Check this description if it clearly says using Slicer to perform DTI processing, tractography or visualization. For example, in reference (Bakhshmand, et al. 2017), there is a sentence “After that, 3D Slicer was used to create interim DTI images and compute the full brain tractography.” If it is not entirely clear from the brief description, find the full text of the paper and check. # # After making sure that a reference cites SlicerDMRI, export the bib file from GoogleScholar. Check if the bibtex includes the full author list. For a paper with many authors, GoogleScholar cuts off the last few authors and use ‘others’ instead. If this happens, correct it by using the full author list. # # Add the bibtex into the SlicerTractReference.bib file. # # After finishing search, commit the changes to the slicerdmri.github.io repository. # ######################################################################################## %% Updated on June/24/2019 for Year 2018 and Year 2019 %% Keyword 'SlicerDMRI' @article{o2019advances, title={Advances in computational and statistical diffusion MRI}, author={O'Donnell, Lauren J and Daducci, Alessandro and Wassermann, Demian and Lenglet, Christophe}, journal={NMR in Biomedicine}, volume={32}, number={4}, pages={e3805}, year={2019}, publisher={Wiley Online Library} } @article{zhang2019mk, title={MK-curve-Characterizing the relation between mean kurtosis and alterations in the diffusion MRI signal}, author={Zhang, Fan and Ning, Lipeng and O'Donnell, Lauren J and Pasternak, Ofer}, journal={NeuroImage}, volume={196}, pages={68--80}, year={2019}, publisher={Elsevier} } @article{zhang2019test, title={Test--retest reproducibility of white matter parcellation using diffusion MRI tractography fiber clustering}, author={Zhang, Fan and Wu, Ye and Norton, Isaiah and Rathi, Yogesh and Golby, Alexandra J and O'Donnell, Lauren J}, journal={Human brain mapping}, volume={40}, number={10}, pages={3041-3057}, year={2019}, publisher={Wiley Online Library} } @article{stojanovski2019polygenic, title={Polygenic Risk and Neural Substrates of Attention-Deficit/Hyperactivity Disorder Symptoms in Youths With a History of Mild Traumatic Brain Injury}, author={Stojanovski, Sonja and Felsky, Daniel and Viviano, Joseph D and Shahab, Saba and Bangali, Rutwik and Burton, Christie L and Devenyi, Gabriel A and O?Donnell, Lauren J and Szatmari, Peter and Chakravarty, M Mallar and others}, journal={Biological psychiatry}, volume={85}, number={5}, pages={408--416}, year={2019}, publisher={Elsevier} } @inproceedings{zhang2018data, title={A data-driven groupwise fiber clustering atlas for consistent white matter parcellation and anatomical tract identification of subjects across the lifespan}, author={Zhang, Fan and Wu, Ye and Norton, Isaiah and Rathi, Yogesh and Makris, Nikos and O'Donnell, Lauren J}, booktitle={Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM)}, year={2018} } @article{sydnor2018comparison, title={A comparison of three fiber tract delineation methods and their impact on white matter analysis}, author={Sydnor, Valerie J and Rivas-Grajales, Ana Mar{\'\i}a and Lyall, Amanda E and Zhang, Fan and Bouix, Sylvain and Karmacharya, Sarina and Shenton, Martha E and Westin, Carl-Fredrik and Makris, Nikos and Wassermann, Demian and others}, journal={NeuroImage}, volume={178}, pages={318--331}, year={2018}, publisher={Elsevier} } @article{ahmad2018region, title={Region-Specific Microstructure in the Neonatal Ventricles of a Porcine Model}, author={Ahmad, Faizan and Soe, Shwe and White, N and Johnston, R and Khan, I and Liao, J and Jones, Michael and Prabhu, R and Maconochie, I and Theobald, Peter}, journal={Annals of biomedical engineering}, volume={46}, number={12}, pages={2162--2176}, year={2018}, publisher={Springer}, comment={only mentioned ONCE in "3D Slicer software plug-in ‘SlicerDMRI’ was used to perform unscented Kalman filter tractography and scalar measurements."} } @article{grant2018altered, title={Altered White Matter Organization in the TUBB3 E410K Syndrome}, author={Grant, P Ellen and Im, Kiho and Ahtam, Banu and Laurentys, Cynthia T and Chan, Wai-Man and Brainard, Maya and Chew, Sheena and Drottar, Marie and Robson, Caroline D and Drmic, Irene and others}, journal={Cerebral Cortex}, year={2018}, comment={mentioned ONCE in "The CC was divided into five equal segments and 3DSlicer’s SlicerDMRI project (dmri.slicer.org) (Norton et al. 2017) was used to view the CC organization using both ellipsoids and tracts. "} } @article{wu2018investigation, title={Investigation into local white matter abnormality in emotional processing and sensorimotor areas using an automatically annotated fiber clustering in major depressive disorder}, author={Wu, Ye and Zhang, Fan and Makris, Nikos and Ning, Yuping and Norton, Isaiah and She, Shenglin and Peng, Hongjun and Rathi, Yogesh and Feng, Yuanjing and Wu, Huawang and others}, journal={NeuroImage}, volume={181}, pages={16--29}, year={2018}, publisher={Elsevier} } @article{dalamagkas2018individual, title={Individual variations of the human corticospinal tract and its hand-related motor fibers using diffusion MRI tractography}, author={Dalamagkas, Kyriakos and Tsintou, Magdalini and Rathi, Yogesh and O?Donnell, Lauren J and Pasternak, Ofer and Gong, Xue and Zhu, Anne and Savadjiev, Peter and Papadimitriou, George M and Kubicki, Marek and others}, journal={Brain imaging and behavior}, pages={1--19}, year={2018}, publisher={Springer} } @article{ahmad2018establishing, title={Establishing the material parameters of the neonatal porcine ventricular myocardium}, author={Ahmad, Faizan}, year={2018}, comment={mentioned TWICE in "The 3D Slicer software plugin ‘SlicerDMRI’ was used to perform unscented Kalman filter (UKF) tractography and scalar measurements." and "The ‘SlicerDMRI’ plugin was also used to select the fibre bundles in each region, which were used to label the map and quantifying the regional-specific FA, within the anterior aspect of both ventricles (Figure 3.7). "} } %% Keyword "Slicer DTI" @inproceedings{liu2019automatic, title={An Automatic Preoperative Path-Planning Algorithm for Neurosurgery Using Combined MRI and DTI}, author={Liu, Jia and Li, Miao and Chen, Fang and Pan, Changcun and Zhang, Xinran and Zhang, Liwei and Liao, Hongen}, booktitle={World Congress on Medical Physics and Biomedical Engineering 2018}, pages={815--819}, year={2019}, organization={Springer}, comment={"Fiber tractography of DTI can be completed using 3D slicer."} } @article{nishioka2019sequential, title={Sequential phases of RGC axonal and somatic injury in EAE mice examined using DTI and OCT}, author={Nishioka, Christopher and Liang, Hsiao-Fang and Barsamian, Barsam and Sun, Shu-Wei}, journal={Multiple sclerosis and related disorders}, volume={27}, pages={315--323}, year={2019}, publisher={Elsevier}, comment={"Corrected image sets were then loaded into 3D Slicer, where eigenvalues derived from the diffusion tensor were used to calculate AD, TR, RD and FA, defined by the following equations...."} } @article{garcia2019prediction, title={Prediction of Laterality in Temporal Lobe Epilepsy Using White Matter Diffusion Metrics}, author={Garc{\'\i}a-Pallero, Mar{\'\i}a A and Hodaie, Mojgan and Zhong, Jidan and Manzanares-Soler, Rafael and Navas, Marta and Pastor, Jes{\'u}s and Vega-Zelaya, Lorena and Delgado-Fern{\'a}ndez, Juan and Sola, Rafael G and Torres, Cristina V}, journal={World neurosurgery}, year={2019}, publisher={Elsevier}, comment={mentioned "DTI" and "3D slicer" mutiple times, "All image processing and tractography analyses were completed using 3D Slicer software.10 Diffusion data were corrected for eddy current and motion distortions using FSL software11 and imported into 3D Slicer, where the DTI volume was calculated. "} } @article{nishioka2019amyloid, title={Amyloid-beta induced retrograde axonal degeneration in a mouse tauopathy model}, author={Nishioka, Christopher and Liang, Hsiao-Fang and Barsamian, Barsam and Sun, Shu-Wei}, journal={NeuroImage}, volume={189}, pages={180--191}, year={2019}, publisher={Elsevier}, comment={"Corrected image sets were then loaded into 3D Slicer, and DTI maps including fractional anisotropy (FA), trace of diffusion (TR), axial diffusion (AxD) and radial diffusion (RAD) were created."} } @article{epprecht2019super, title={Super-resolution Diffusion Tensor Imaging for Delineating the Facial Nerve in Patients with Vestibular Schwannoma}, author={Epprecht, Lorenz and Kozin, Elliott D and Piccirelli, Marco and Kanumuri, Vivek V and Tarabichi, Osama and Remenschneider, Aaron and Barker II, Frederick G and McKenna, Michael J and Huber, Alexander M and Cunnane, Marybeth E and others}, journal={Journal of Neurological Surgery Part B: Skull Base}, year={2019}, publisher={Georg Thieme Verlag KG}, comment={"3D visualizations of tumor and tracts were performed in 3D slicer (version 4.8, www.slicer.org, Boston, Massachusetts, United States)."} } @article{girault2019white, title={White matter microstructural development and cognitive ability in the first 2 years of life}, author={Girault, Jessica B and Cornea, Emil and Goldman, Barbara D and Knickmeyer, Rebecca C and Styner, Martin and Gilmore, John H}, journal={Human Brain Mapping}, volume={40}, number={4}, pages={1195--1210}, year={2019}, publisher={Wiley Online Library}, comment={"A total of 45 homologous tracts were defined in both atlases using streamline deterministic tractography in 3D Slicer (http://www.slicer.org). "} } @article{rasmussen2019maternal, title={Maternal Interleukin-6 concentration during pregnancy is associated with variation in frontolimbic white matter and cognitive development in early life}, author={Rasmussen, Jerod M and Graham, Alice M and Entringer, Sonja and Gilmore, John H and Styner, Martin and Fair, Damien A and Wadhwa, Pathik D and Buss, Claudia}, journal={NeuroImage}, volume={185}, pages={825--835}, year={2019}, publisher={Elsevier}, comment={"Fiber tract streamline DTI tractography was performed via 3D Slicer (version 4.3.0) (http://www.slicer.org) in the DTI atlas space followed by fiber cleaning with FiberViewerLight (www.nitric.org/projects/fwlight). "} } @article{del2019diffusion, title={Diffusion abnormalities in the corpus callosum in first episode schizophrenia: Associated with enlarged lateral ventricles and symptomatology}, author={del Re, Elisabetta C and Bouix, Sylvain and Fitzsimmons, Jennifer and Blokland, Gabri{\"e}lla AM and Mesholam-Gately, Raquelle and Wojcik, Joanne and Kikinis, Zora and Kubicki, Marek and Petryshen, Tracey and Pasternak, Ofer and others}, journal={Psychiatry research}, year={2019}, publisher={Elsevier}, comment={"In reconstructing regions of interest (ROIs), tensors were estimated by the least squares method (Basser and Jones, 2002) using 3DSlicer software version 4.3.1 (http://www.slicer.org/) (Pieper et al., 2004, Pieper et al., 2006)."} } @article{ahn2019white, title={White matter development in infants at risk for schizophrenia}, author={Ahn, Sung Jun and Cornea, Emil and Murphy, Veronica and Styner, Martin and Jarskog, L Fredrik and Gilmore, John H}, journal={Schizophrenia research}, year={2019}, publisher={Elsevier}, comment={"....on which a total of 45 fiber tract segments consistent with reference were reconstructed using streamline tractography using 3D Slicer (https://www.slicer.org)."} } @article{gicas2019diffusion, title={Diffusion tensor imaging of neurocognitive profiles in a community cohort living in marginal housing}, author={Gicas, Kristina M and Cheng, Alex and Rawtaer, Iris and Willi, Taylor S and Panenka, William J and Lang, Donna J and Smith, Geoff N and Vila-Rodriguez, Fidel and Leonova, Olga and Giesbrecht, Chantelle J and others}, journal={Brain and behavior}, volume={9}, number={3}, pages={e01233}, year={2019}, publisher={Wiley Online Library}, comment={"DTI fitting was run using a nonlinear least squares approach with shifted negative eigenvalues from 3D Slicer."} } @article{howell2019disentangling, title={Disentangling the effects of early caregiving experience and heritable factors on brain white matter development in rhesus monkeys}, author={Howell, Brittany R and Ahn, Mihye and Shi, Yundi and Godfrey, Jodi R and Hu, Xiaoping and Zhu, Hongtu and Styner, Martin and Sanchez, Mar M}, journal={NeuroImage}, volume={197}, pages={625--642}, year={2019}, publisher={Elsevier}, comment={"Tensor computation employed a weighted least square estimation to produce a diffusion tensor image for each subject. Each DTI dataset was further assessed visually for artifacts with 3D Slicer (Fedorov et al., 2012) and was excluded if any artifact could not be corrected. "} } @article{di2019neuroimaging, title={Neuroimaging auditory verbal hallucinations in schizophrenia patient and healthy populations}, author={Di Biase, Maria Angelique and Zhang, Fan and Lyall, Amanda and Kubicki, Marek and Mandl, Ren{\'e} CW and Sommer, Iris E and Pasternak, Ofer}, journal={Psychological medicine}, pages={1--10}, year={2019}, publisher={Cambridge University Press} } @inproceedings{mujika2018software, title={Software applications for the digital management radiological images in the study of the corticospinal tract}, author={Mujika, Katrin Muradas and M{\'e}ndez, Juan A Juanes and de Miguel, Andr{\'e}s Frami{\~n}{\'a}n}, booktitle={Proceedings of the Sixth International Conference on Technological Ecosystems for Enhancing Multiculturality}, pages={381--385}, year={2018}, organization={ACM}, comment={" The 2D DTI obtained with 3D Slicer has a lower resolution than the image obtained with the other software program."} } @article{park2018radiomics, title={Radiomics and machine learning may accurately predict the grade and histological subtype in meningiomas using conventional and diffusion tensor imaging}, author={Park, Yae Won and Oh, Jongmin and You, Seng Chan and Han, Kyunghwa and Ahn, Sung Soo and Choi, Yoon Seong and Chang, Jong Hee and Kim, Se Hoon and Lee, Seung-Koo}, journal={European radiology}, pages={1--9}, year={2018}, publisher={Springer}, comment={"T1C image and DTI data were processed with a multi-platform, free, and open-source software package for visualization and medical image computing (3D slicer, version 4.6.2-1; available at: http://slicer.org/)"} } @article{castano2018can, title={What can be learned from diffusion tensor imaging from a large traumatic brain injury cohort?: white matter integrity and its relationship with outcome}, author={Castano Leon, Ana Maria and Cicuendez, Marta and Navarro, Blanca and Munarriz, Pablo M and Cepeda, Santiago and Paredes, Igor and Hilario, Amaya and Ramos, Ana and G{\'o}mez, Pedro Antonio and Lagares, Alfonso}, journal={Journal of neurotrauma}, volume={35}, number={20}, pages={2365--2376}, year={2018}, publisher={Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~…}, comment={"DWIs were transferred to a freely supplied SLICER 4.2.2-1 workstation to generate DTI and FA maps."} } @inproceedings{cardona2018influence, title={Influence of Realistic Head Modeling on EEG Forward Problem}, author={Cardona, H{\'e}ctor Fabio Torres and Acosta, Carlos Daniel and Dominguez, German Castellanos}, booktitle={Brain Informatics: International Conference, BI 2018, Arlington, TX, USA, December 7--9, 2018, Proceedings}, volume={11309}, pages={32}, year={2018}, organization={Springer}, comment={"Image preprocessing was performed using 3D Slicer built-in modules." " We use diffusion tensor imaging (DTI) data to determine the conductivity tensors in the WM compartment"} } @article{rostowksy2018macroscale, title={Macroscale White Matter Alterations Due to Traumatic Cerebral Microhemorrhages Are Revealed by Diffusion Tensor Imaging}, author={Rostowksy, Kenneth A and Maher, Alexander S and Irimia, Andrei}, journal={Frontiers in Neurology}, volume={9}, pages={948}, year={2018}, publisher={Frontiers}, comment={"DWI volumes were processed in TrackVis (http://trackvis.org) and 3D Slicer (http://www.slicer. org). Tensors were fit to DWI data to perform DTI, and tractography streamlines were reconstructed using deterministic tractography subject to the following parameters...."} } @article{joo2018altered, title={Altered white matter connectivity in patients with schizophrenia: An investigation using public neuroimaging data from SchizConnect}, author={Joo, Sung Woo and Yoon, Woon and Shon, Seung-Hyun and Kim, Harin and Cha, Saetbyeol and Park, Kee Jeong and Lee, Jungsun}, journal={PloS one}, volume={13}, number={10}, pages={e0205369}, year={2018}, publisher={Public Library of Science}, comment={"We used UKF tractography implemented in the 3D Slicer (http://www.slicer.org) [35] to perform whole-brain tractography."} } @article{lepage2018white, title={White matter abnormalities in mild traumatic brain injury with and without post-traumatic stress disorder: a subject-specific diffusion tensor imaging study}, author={Lepage, Christian and de Pierrefeu, Amicie and Koerte, Inga K and Coleman, Michael J and Pasternak, Ofer and Grant, Gerald and Marx, Christine E and Morey, Rajendra A and Flashman, Laura A and George, Mark S and others}, journal={Brain imaging and behavior}, volume={12}, number={3}, pages={870--881}, year={2018}, publisher={Springer}, comment={"We used traditional analyses of DTI, as described below", "We used 3D Slicer version 4.5 (Surgical Planning Laboratory, Brigham and Women's Hospital, Boston, USA) for visual inspections"} } %% Keyword "Slicer Tractography" @inproceedings{chudzik2019dti, title={DTI Helps to Predict Parkinson?s Patient?s Symptoms Using Data Mining Techniques}, author={Chudzik, Artur and Szyma{\'n}ski, Artur and Nowacki, Jerzy Pawe{\l} and Przybyszewski, Andrzej W}, booktitle={Asian Conference on Intelligent Information and Database Systems}, pages={615--623}, year={2019}, organization={Springer}, comment={"Parameters had been obtained from 3DSlicer (Harvard Medical School, Boston, MA), which allowed us to track connections between the stimulated part of STN and the cortex based on the DTI (diffusion tensor imaging)."} } @article{tohyama2018early, title={Early postsurgical diffusivity metrics for prognostication of long-term pain relief after Gamma Knife radiosurgery for trigeminal neuralgia}, author={Tohyama, Sarasa and Hung, Peter Shih-Ping and Zhong, Jidan and Hodaie, Mojgan}, journal={Journal of neurosurgery}, volume={1}, number={aop}, pages={1--10}, year={2018}, publisher={American Association of Neurological Surgeons}, comment={"single tensor tractography was performed for long-term responders and nonresponders. For each patient, both pre- and 6-month posttreatment DTI was acquired and tracts were reconstructed using 3D Slicer version 4.4.0"} } @article{joo2018abnormal, title={Abnormal asymmetry of white matter tracts between ventral posterior cingulate cortex and middle temporal gyrus in recent-onset schizophrenia}, author={Joo, Sung Woo and Chon, Myong-Wuk and Rathi, Yogesh and Shenton, Martha E and Kubicki, Marek and Lee, Jungsun}, journal={Schizophrenia research}, volume={192}, pages={159--166}, year={2018}, publisher={Elsevier}, comment={"Using UKF tractography (Rathi et al., 2011), whole brain tractography was performed."} } @misc{korting2018determination, title={Determination of In-vivo Muscle Architecture: Comparison of Ultrasound and Diffusion Tensor Imaging and Analysis of Muscle Morphology in Post-stroke Patients}, author={K{\"o}rting, Clara}, year={2018}, comment={"for this project was carried out manually for each patient using the open source platform 3D Slicer" , "the produced diffusion parameters of the filter better reflect the characteristics of the tissue and that tractography results could be improved"} } %% Updated on May/16/2018 for Year 2018 %% Keyword 'SlicerDMRI' @article{gong2018free, title={Free water modeling of peritumoral edema using multi-fiber tractography: Application to tracking the arcuate fasciculus for neurosurgical planning}, author={Gong, Shun and Zhang, Fan and Norton, Isaiah and Essayed, Walid I and Unadkat, Prashin and Rigolo, Laura and Pasternak, Ofer and Rathi, Yogesh and Hou, Lijun and Golby, Alexandra J and others}, journal={PloS one}, volume={13}, number={5}, pages={e0197056}, year={2018}, publisher={Public Library of Science}, comment={Then the 3D Slicer (www.slicer.org) [40,41] SlicerDMRI extension (dmri.slicer.org) [42] was applied to obtain baseline images (B0, the b = 0 image from the DWI) and derive binary brain masks from the DWI images.} } @article{lyall2018utilizing, title={Utilizing Mutual Information Analysis to Explore the Relationship Between Gray and White Matter Structural Pathologies in Schizophrenia}, author={Lyall, Amanda E and Savadjiev, Peter and del Re, Elisabetta C and Seitz, Johanna and O'Donnell, Lauren J and Westin, Carl-Fredrik and Mesholam-Gately, Raquelle I and Petryshen, Tracey and Wojcik, Joanne D and Nestor, Paul and others}, journal={Schizophrenia bulletin}, year={2018}, comment={All visualization of diffusion MRI data was performed in 3D Slicer (www.slicer.org) via the SlicerDMRI project (dmri.slicer.org).} } @article{stefanik2018brain, title={Brain-Behavior Participant Similarity Networks Among Youth and Emerging Adults with Schizophrenia Spectrum, Autism Spectrum, or Bipolar Disorder and Matched Controls}, author={Stefanik, Laura and Erdman, Lauren and Ameis, Stephanie H and Foussias, George and Mulsant, Benoit H and Behdinan, Tina and Goldenberg, Anna and O'Donnell, Lauren J and Voineskos, Aristotle N}, journal={Neuropsychopharmacology}, volume={43}, number={5}, pages={1180}, year={2018}, publisher={Nature Publishing Group}, comment={In this study, we performed the tractography algorithm and visualization of the results in 3D Slicer 1[15] via the SlicerDMRI project 2} } @inproceedings{fukuda2018reconstruction, title={Reconstruction of 3D Muscle Fiber Structure Using High Resolution Cryosectioned Volume}, author={Fukuda, Norio and O'Donnell, Lauren J and Westin, Carl-Fredrik and Takao, Masaki and Sugano, Nobuhiko and Chung, Beom Sun and Park, Jin Seo and Sato, Yoshinobu}, booktitle={Computational Methods and Clinical Applications in Musculoskeletal Imaging: 5th International Workshop, MSKI 2017, Held in Conjunction with MICCAI 2017, Quebec City, QC, Canada, September 10, 2017, Revised Selected Papers}, volume={10734}, pages={85}, year={2018}, organization={Springer}, comment={In this study, we performed the tractography algorithm and visualization of the results in 3D Slicer1 [15] via the SlicerDMRI project2} } %% Keyword 'Slicer Tractography' @article{mujika2018advantages, title={Advantages and Disadvantages in Image Processing with Free Software in Radiology}, author={Mujika, Katrin Muradas and M{\'e}ndez, Juan Antonio Juanes and de Miguel, Andr{\'e}s Frami{\~n}an}, journal={Journal of medical systems}, volume={42}, number={3}, pages={36}, year={2018}, publisher={Springer}, comment={Fig. 3 Image processing to obtain a tractography image with 3D Slicer.} } @article{lee2018timing, title={The timing of stereotactic radiosurgery for medically refractory trigeminal neuralgia: the evidence from diffusion tractography images}, author={Lee, Cheng-Chia and Chong, Shin Tai and Chen, Ching-Jen and Hung, Sheng-Che and Yang, Huai-Che and Lin, Chung-Jung and Wu, Chih-Chun and Chung, Wen-Yuh and Guo, Wan-Yuo and Pan, David Hung-Chi and others}, journal={Acta neurochirurgica}, volume={160}, number={5}, pages={977--986}, year={2018}, publisher={Springer}, comment={The software package Slicer (A work of National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant U54 EB005149) was used to pre-process the DTI dataset (including eddy-current correction, head motion correction, diffusion gradient direction correction, skull stripping, DTI indices calculation, and image flipping)} } @article{wang2018automatic, title={Automatic quantification of microscopic heart damage in a mouse model of {Duchenne} muscular dystrophy using optical polarization tractography}, author={Wang, Yuanbo and Ravanfar, Mohammadreza and Zhang, Keqing and Duan, Dongsheng and Yao, Gang}, journal={Journal of biophotonics}, year={2018}, publisher={Wiley Online Library}, comment={The 3D visualization was created using the 3DSlicer software (www.slicer.org).} } @article{xiao2018nonlinear, title={Nonlinear deformation of tractography in ultrasound-guided low-grade gliomas resection}, author={Xiao, Yiming and Eikenes, Live and Reinertsen, Ingerid and Rivaz, Hassan}, journal={International journal of computer assisted radiology and surgery}, pages={1--11}, year={2018}, publisher={Springer}, comment={All the surgical data, including T2 FLAIR MRIs, segmented tumors, and the white matter tracts, were nonlinearly warped by deformation fields from MRI?US registration. The results were visualized with the software 3DSlicer [46]} } @article{paniandi2018mr, title={MR neurography of median nerve using diffusion tensor imaging {(DTI)} and its efficacy to diagnose carpal tunnel syndrome in Malaysian population.}, author={Paniandi, Vikneswary and George, John and Goh, Khean Jin and Tan, Li Kuo}, journal={Neurology Asia}, volume={23}, number={1}, year={2018}, comment={Magnetic resonance imaging (MRI) wrist was performed with pre-set axial PD and DTI protocol on a 3T MRI, images post-processed using 3D SLICER software to generate median nerve tract and measure diffusion parameters FA, MD, AD and RD in segments and focal points.} } @article{swanson2018development, title={Development of White Matter Circuitry in Infants With Fragile {X} Syndrome}, author={Swanson, Meghan R and Wolff, Jason J and Shen, Mark D and Styner, Martin and Estes, Annette and Gerig, Guido and McKinstry, Robert C and Botteron, Kelly N and Piven, Joseph and Hazlett, Heather C}, journal={JAMA psychiatry}, volume={75}, number={5}, pages={505--513}, year={2018}, publisher={American Medical Association}, comment={Nineteen white matter fiber tracts were generated using seed label maps in the combined atlas space in 3D Slicer according to existing tractography methods (https://www.slicer.org).} } @article{li2018investigation, title={Investigation of Ginkgo biloba extract ({EGb} 761) promotes neurovascular restoration and axonal remodeling after embolic stroke in rat using magnetic resonance imaging and histopathological analysis}, author={Li, Man-Zhong and Zhang, Yi and Zou, Hai-Yan and Ouyang, Jun-Yao and Zhan, Yu and Yang, Le and Cheng, Brian Chi-Yan and Wang, Lei and Zhang, Qiu-Xia and Lei, Jian-Feng and others}, journal={Biomedicine \& Pharmacotherapy}, volume={103}, pages={989--1001}, year={2018}, publisher={Elsevier}, comment={To visualize the fiber orientation and integrity, diffusion tensor tractography (DTT) wasperformed using Slicer 3D software (https://www.slicer.org).} } @article{li2018effects, title={Effects of total saponins from Trillium tschonoskii rhizome on grey and white matter injury evaluated by quantitative multiparametric MRI in a rat model of ischemic stroke}, author={Li, Manzhong and Ouyang, Junyao and Zhang, Yi and Cheng, Brian Chi Yan and Zhan, Yu and Yang, Le and Zou, Haiyan and Zhao, Hui}, journal={Journal of ethnopharmacology}, year={2018}, publisher={Elsevier}, comment={o determine the orientation and integrity of fibre systems, fibre tractography was conducted using three-dimensional (3D) Slicer software (https://www.slicer.org).} } @article{rivas2018sexually, title={Sexually dimorphic structural abnormalities in major connections of the medial forebrain bundle in alcoholism}, author={Rivas-Grajales, Ana Mar{\'\i}a and Sawyer, Kayle S and Karmacharya, Sarina and Papadimitriou, George and Camprodon, Joan A and Harris, Gordon J and Kubicki, Marek and Oscar-Berman, Marlene and Makris, Nikos}, journal={NeuroImage: Clinical}, volume={19}, pages={98--105}, year={2018}, publisher={Elsevier}, comment={Diffusion tensor images were estimated from the Diffusion-Weighted Images (DWI) in Slicer Version 4 (http://www.slicer.org), based on the weighted-least-squares estimation.} } @article{rasmussen2018maternal, title={Maternal Interleukin-6 concentration during pregnancy is associated with variation in frontolimbic white matter and cognitive development in early life}, author={Rasmussen, Jerod M and Graham, Alice M and Entringer, Sonja and Gilmore, John H and Styner, Martin and Fair, Damien A and Wadhwa, Pathik D and Buss, Claudia}, journal={NeuroImage}, year={2018}, publisher={Elsevier}, comment={Fiber tract streamline DTI tractography was performed via 3D Slicer (version 4.3.0) (http://www.slicer.org) in the DTI atlas space.} } @article{krogsrud2018development, title={Development of white matter microstructure in relation to verbal and visuospatial working memory?A longitudinal study}, author={Krogsrud, Stine K and Fjell, Anders M and Tamnes, Christian K and Grydeland, H{\aa}kon and Due-T{\o}nnessen, Paulina and Bj{\o}rnerud, Atle and Sampaio-Baptista, Cassandra and Andersson, Jesper and Johansen-Berg, Heidi and Walhovd, Kristine B}, journal={PloS one}, volume={13}, number={4}, pages={e0195540}, year={2018}, publisher={Public Library of Science}, comment={Color codes refer to: Light blue: Inferior longitudinal fasciculus (ILF), Yellow: Inferior fronto-occipital fasciculus (IFOF), Red: Forceps major (FMaj), Blue: Superior longitudinal fasciculus (SLF), Green: Uncinate fasciculus (UF), and Purple: Forceps minor (FMin). The 3D figures were made by the use of Slicer (http://www.slicer.org/). L = left and R = right.} } @article{kubicki2018lifespan, title={Lifespan Trajectories of White Matter Changes in Rhesus Monkeys}, author={Kubicki, M and Baxi, M and Pasternak, O and Tang, Y and Karmacharya, S and Chunga, N and Lyall, AE and Rathi, Y and Eckbo, R and Bouix, S and others}, journal={Cerebral Cortex}, year={2018}, comment={Following these preprocessing steps, FA was estimated using least square fit Slicer procedure. FW and the FA of the tissue (FAt) were also calculated for each voxel using in house software (Pasternak et al. 2009) (see Supplemental material for an axial section of the FA, FAt and FW maps).} } @article{mayinger2018white, title={White matter alterations in college football players: a longitudinal diffusion tensor imaging study}, author={Mayinger, Michael Christian and Merchant-Borna, Kian and Hufschmidt, Jakob and Muehlmann, Marc and Weir, Isabelle Ruth and Rauchmann, Boris-Stephan and Shenton, Martha Elizabeth and Koerte, Inga Katharina and Bazarian, Jeffrey John}, journal={Brain imaging and behavior}, volume={12}, number={1}, pages={44--53}, year={2018}, publisher={Springer}, comment={DTI data sets were visually inspected for image quality using 3D Slicer version 4.3.0 (http://www.slicer.org; Surgical Planning Laboratory, Brigham and Women?s Hospital, Boston, MA) (Fedorov et al. 2012).} } %% Keyword 'Slicer DTI' @article{lee2018f186, title={F186. Tapetum Abnormalities In First-episode Psychosis And Relationship To Symptom Severity And Duration Of Untreated Psychosis}, author={Lee, Sun Woo and Lee, Arira and Lee, Kang-Soo and Kim, Jeong Hoon and Lee, Sang-Hyuk}, journal={Schizophrenia Bulletin}, volume={44}, number={Suppl 1}, pages={S293}, year={2018}, publisher={Oxford University Press}, comment={Tapetum, region of interest was extracted using 3D slicer and tract-based spatial statistics (TBSS) were used for DTI analysis.} } @article{lee2018diagnostic, title={Diagnostic value of structural and diffusion imaging measures in schizophrenia}, author={Lee, Jungsun and Chon, Myong-Wuk and Kim, Harin and Rathi, Yogesh and Bouix, Sylvain and Shenton, Martha E and Kubicki, Marek}, journal={NeuroImage: Clinical}, volume={18}, pages={467--474}, year={2018}, publisher={Elsevier}, comment={Using Slicer V. 4.4 and an in-house program, we estimated FA and Trace (TR, equal to 3*MD) images from DTI images} } @article{sollmann2018sex, title={Sex differences in white matter alterations following repetitive subconcussive head impacts in collegiate ice hockey players}, author={Sollmann, Nico and Echlin, Paul S and Schultz, Vivian and Viher, Petra V and Lyall, Amanda E and Tripodis, Yorghos and Kaufmann, David and Hartl, Elisabeth and Kinzel, Philipp and Forwell, Lorie A and others}, journal={Neuroimage: clinical}, volume={17}, pages={642--649}, year={2018}, publisher={Elsevier}, comment={First, quality checks were performed by visually inspecting diffusion-weighted data sets using 3D Slicer (http://www.slicer.org; version 4.5.0-1, Surgical Planning Laboratory, Brigham and Women's Hospital, Boston, MA, USA) (Fedorov et al., 2012).} } @article{karmacharya2018advanced, title={Advanced diffusion imaging for assessing normal white matter development in neonates and characterizing aberrant development in congenital heart disease}, author={Karmacharya, S and Gagoski, B and Ning, L and Vyas, R and Cheng, HH and Soul, J and Newberger, JW and Shenton, ME and Rathi, Y and Grant, PE}, journal={NeuroImage: Clinical}, year={2018}, publisher={Elsevier}, comment={Diffusion tensors were estimated at each voxel in Slicer Version 4 (http://www.slicer.org), using weighted linear least squares fitting } } %% Updated on Jan/21/2018 for Year 2017 and 2018 (a few) %% Keyword 'SlicerDMRI' @article{albi2018image, title={Image Registration to Compensate for {EPI} Distortion in Patients with Brain Tumors: An Evaluation of Tract-Specific Effects}, author={Albi, Angela and Meola, Antonio and Zhang, Fan and Kahali, Pegah and Rigolo, Laura and Tax, Chantal M.W. and Ciris, Pelin Aksit and Essayed, Walid I. and Unadkat, Prashin and Norton, Isaiah and Rathi, Yogesh and Olubiyi, Olutayo and Golby, Alexandra J. and O'Donnell, Lauren J.}, journal={Journal of Neuroimaging}, year={2018}, publisher={Wiley Online Library} } @article {zhang2018supra, title = {Suprathreshold fiber cluster statistics: Leveraging white matter geometry to enhance tractography statistical analysis}, journal = {NeuroImage}, year = {2018}, volume = {171}, url = {https://www.sciencedirect.com/science/article/pii/S1053811918300065}, author = {Zhang, Fan and Wu, Weining and Ning, Lipeng and McAnulty, Gloria and Waber, Deborahand and Gagoski, Borjan and Sarill, Kiera and Hamoda, Hesham and Song, Yang and Cai, Weidong and Rathi, Yogesh and O'Donnell, Lauren J.} } @article {Zhang2017Whole, title = {Whole brain white matter connectivity analysis using machine learning: An application to autism}, journal = {NeuroImage}, year = {2017}, url = {https://www.sciencedirect.com/science/article/pii/S105381191730856X}, author = {Zhang, Fan and Savadjiev, Peter and Cai, Weidong and Song, Yang and Rathi, Yogesh and Tunc, Birkan and Parker, Drew and Kapur, Tina and Schultz, Robert T. and Makris, Nikos and Verma, Ragini and O'Donnell, Lauren J.} } @phdthesis{stefanik2017behavioural, title={The Behavioural and Neural Correlates of Social Cognition: A Dimensional Approach in Youth with Mental Illness}, author={Stefanik, Laura Nicole}, year={2017}, school={University of Toronto}, comment={DWI scans were preprocessed using DTIPrep (Oguz et al., 2014), and tensors and fiber tracts were generated via the SlicerDMRI project (https://github.com/SlicerDMRI), funded by NIH U01 CA199459} } @article{essayed2017white, title = {White matter tractography for neurosurgical planning: A topography-based review of the current state of the art}, journal = {NeuroImage: Clinical}, volume = {15}, year = {2017}, pages = {659-672}, doi = {https://doi.org/10.1016/j.nicl.2017.06.011}, url = {http://www.sciencedirect.com/science/article/pii/S2213158217301444}, author = {Essayed, Walid I. and Zhang, Fan and Unadkat, Prashin and G. Rees Cosgrove and Golby, Alexandra J. and O'Donnell, Lauren J.} } @conference {zhang2017supra, title = {Supra-threshold Fiber Cluster Statistics for Data-driven Whole Brain Tractography Analysis}, booktitle = {International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)}, volume = {10433}, year = {2017}, pages = {556-565}, author = {Zhang, Fan and Wu, Weining and Lipeng Ning and McAnulty, Gloria and Waber, Deborahand and Gagoski, Borjan and Sarill, Kiera and Hamoda, Hesham and Song, Yang and Cai, Weidong and Rathi, Yogesh and O'Donnell, Lauren J.} } @article{norton2017slicerdmri, title={SlicerDMRI: open source diffusion MRI software for brain cancer Research}, author={Norton, Isaiah and Essayed, Walid Ibn and Zhang, Fan and Sonia Pujol and Yarmarkovich, Alex and Golby, Alexandra J and Kindlmann, Gordon and Wasserman, Demian and Johnson, J. and Westin, Carl-Fredrik and O'Donnell, Lauren J}, journal={Cancer research}, volume={77}, number={21}, pages={e101--e103}, year={2017}, publisher={AACR} } @article{stefanik2017brain, title={Brain-Behavior Participant Similarity Networks Among Youth and Emerging Adults with Schizophrenia Spectrum, Autism Spectrum, or Bipolar Disorder and Matched Controls}, author={Stefanik, Laura and Erdman, Lauren and Ameis, Stephanie H and Foussias, George and Mulsant, Benoit H and Behdinan, Tina and Goldenberg, Anna and O'Donnell, Lauren J and Voineskos, Aristotle N}, journal={Neuropsychopharmacology}, year={2017}, publisher={Nature Publishing Group}, comment={For white matter analyses, tensors and fiber tracts were generated in 3D Slicer (Fedorov et al, 2012) via the SlicerDMRI project (dmri.slicer.org; Norton et al, 2017) and an automated method was used for tractography segmentation (dmri.slicer.org/whitematteranalysis).} } @inproceedings{otake2017patient, title={Patient-Specific Skeletal Muscle Fiber Modeling from Structure Tensor Field of Clinical CT Images}, author={Otake, Yoshito and Yokota, Futoshi and Fukuda, Norio and Takao, Masaki and Takagi, Shu and Yamamura, Naoto and O'Donnell, Lauren J and Westin, Carl-Fredrik and Sugano, Nobuhiko and Sato, Yoshinobu}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={656--663}, year={2017}, organization={Springer}, comment={We applied tractography in 3D Slicer (www.slicer.org) [5] via the SlicerDMRI project (dmri.slicer.org) to the structure tensor field.} } @article{liao2017performance, title={Performance of unscented Kalman filter tractography in edema: Analysis of the two-tensor model}, author={Liao, Ruizhi and Ning, Lipeng and Chen, Zhenrui and Rigolo, Laura and Gong, Shun and Pasternak, Ofer and Golby, Alexandra J and Rathi, Yogesh and O'Donnell, Lauren J}, journal={NeuroImage: Clinical}, volume={15}, pages={819--831}, year={2017}, publisher={Elsevier} } @article{o2017advances, title={Advances in computational and statistical diffusion MRI}, author={O'Donnell, Lauren J and Daducci, Alessandro and Wassermann, Demian and Lenglet, Christophe}, journal={NMR in Biomedicine}, year={2017}, publisher={Wiley Online Library}, comment={These images were created using the first dataset from the Human Connectome Project[12] using the SlicerDMRI package in 3D Slicer[13, 14]} } %% Keyword 'Slicer Tractography' @article{behan2017comparison, title={Comparison of Diffusion-Weighted MRI Reconstruction Methods for Visualization of Cranial Nerves in Posterior Fossa Surgery}, author={Behan, Brendan and Chen, David Q and Sammartino, Francesco and DeSouza, Danielle D and Wharton-Shukster, Erika and Hodaie, Mojgan}, journal={Frontiers in neuroscience}, volume={11}, pages={554}, year={2017}, publisher={Frontiers}, comment={Three distinct reconstruction methods [two tensor-based methods: single diffusion tensor tractography (SDT) (3D Slicer), eXtended streamline tractography (XST), and one fiber orientation distribution (FOD)-based method} } @article{pujol2017vivo, title={In vivo exploration of the connectivity between the subthalamic nucleus and the globus pallidus in the human brain using multi-fiber tractography}, author={Pujol, Sonia and Cabeen, Ryan and S{\'e}bille, Sophie B and Yelnik, J{\'e}r{\^o}me and Fran{\c{c}}ois, Chantal and Fernandez Vidal, Sara and Karachi, Carine and Zhao, Yulong and Cosgrove, G Rees and Jannin, Pierre and others}, journal={Frontiers in neuroanatomy}, volume={10}, pages={119}, year={2017}, publisher={Frontiers}, comment={The cerebral peduncles and posterior limb of the internal capsule were manually segmented in axial cross-sections of the directionally encoded color map derived from the diffusion-weighted images in 3D Slicer.} } @article{pieczewski2017p, title={P 12 Integrating nTMS motor mapping of the M1 tongue area into diffusion tractography to reconstruct motor-speech pathways}, author={Pieczewski, J and Nettekoven, C and Neuschmelting, V and Thiele, K and Hoevels, M and Reck, N and Tittgemeyer, M and Grefkes, C and Goldbrunner, R and Lucas, C Weiss}, journal={Clinical Neurophysiology}, volume={128}, number={10}, pages={e332}, year={2017}, publisher={Elsevier}, comment={Tracts were visualized using MRIcron and Slicer (3D).} } @article{li2017fiber, title={A Fiber Tractography Study of Social-Emotional Related Fiber Tracts in Children and Adolescents with Autism Spectrum Disorder}, author={Li, Yun and Fang, Hui and Zheng, Wenming and Qian, Lu and Xiao, Yunhua and Wu, Qiaorong and Chang, Chen and Xiao, Chaoyong and Chu, Kangkang and Ke, Xiaoyan}, journal={Neuroscience bulletin}, volume={33}, number={6}, pages={722--730}, year={2017}, publisher={Springer}, comment={The 3D Slicer software platform was used to select the five fasciculi as ROIs to perform interactive fiber tractography.} } @article{shany2017diffusion, title={Diffusion tensor tractography of the cerebellar peduncles in prematurely born 7-year-old children}, author={Shany, Eilon and Inder, Terrie E and Goshen, Sharon and Lee, Iris and Neil, Jeffrey J and Smyser, Christopher D and Doyle, Lex W and Anderson, Peter J and Shimony, Joshua S}, journal={The Cerebellum}, volume={16}, number={2}, pages={314--325}, year={2017}, publisher={Springer}, comment={Full brain tractography was filtered using regions of interest (ROIs) manually placed perpendicular to the length of the tract based on anatomical landmarks in native space using Analyze 10 (Mayo Clinic, Rochester MN) and visualized on Slicer 2.5 (http://www.slicer.org/) } } @inproceedings{zhao2017joint, title={Joint Visualization of UKF Tractography Data}, author={Zhao, Wen and Zhang, Wenyao and Wang, Na and Liao, Pin}, booktitle={International Conference on Image and Graphics}, pages={158--169}, year={2017}, organization={Springer}, comment={DWI sample dataset available from 3D Slicer [20]; By seeding in corpus callosum and running UKF tractography algorithm.} } @article{bakhshmand2017multixplore, title={Multixplore: visual exploration platform for multimodal neuroimaging data}, author={Bakhshmand, Saeed M and Khan, Ali R and de Ribaupierre, Sandrine and Eagleson, Roy}, journal={Journal of neuroscience methods}, volume={290}, pages={1--12}, year={2017}, publisher={Elsevier}, comment={After that, 3D Slicer was used to create interim DTI images and compute the full brain tractography} } @article{vicente2017inpainting, title={Inpainting on diffusion weighted magnetic resonance images. An application to tractography of multiple sclerosis patients}, author={Vicente Sola, Alex}, year={2017}, url={https://repositori.upf.edu/handle/10230/32913}, comment={Horizontal plane of brain DTI calculated with 3DSlicer software} } @article{makris2017mapping, title={Mapping temporo-parietal and temporo-occipital cortico-cortical connections of the human middle longitudinal fascicle in subject-specific, probabilistic, and stereotaxic Talairach spaces}, author={Makris, Nikos and Zhu, A and Papadimitriou, GM and Mouradian, P and Ng, I and Scaccianoce, E and Baselli, G and Baglio, F and Shenton, ME and Rathi, Y and Dickerson B. and Yeterian E. and Kubicki M.}, journal={Brain imaging and behavior}, volume={11}, number={5}, pages={1258--1277}, year={2017}, publisher={Springer}, comment={HARDI tractography was performed in 3D-Slicer (v2.7, www.slicer.org), using a multi-tensor tractography algorithm (Malcolm et al. 2010)} } @article{whitford2017deficits, title={Deficits in Cortical Suppression During Vocalization are Associated With Structural Abnormalities in the Arcuate Fasciculus in Early Illness Schizophrenia and Clinical High Risk for Psychosis}, author={Whitford, Thomas J and Oestreich, Lena KL and Ford, Judith M and Roach, Brian J and Loewy, Rachel L and Stuart, Barbara K and Mathalon, Daniel H}, journal={Schizophrenia bulletin}, year={2017}, comment={The Slicer-3 software package (www.slicer.org) was used to extract the 2 fas- ciculi-of-interest namely the arcuate fasciculus and the pyramidal tract} } @article{bakhshmand2017multimodal, title={Multimodal connectivity based eloquence score computation and visualisation for computer-aided neurosurgical path planning}, author={Bakhshmand, Saeed M and Eagleson, Roy and de Ribaupierre, Sandrine}, journal={Healthcare technology letters}, volume={4}, number={5}, pages={152--156}, year={2017}, publisher={IET}, comment={DTI conversion and whole fibre tract generation (tractography) was carried out in 3D Slicer [ https://www.slicer.org/]} } @article{swanson2017splenium, title={Splenium development and early spoken language in human infants}, author={Swanson, Meghan R and Wolff, Jason J and Elison, Jed T and Gu, Hongbin and Hazlett, Heather C and Botteron, Kelly and Styner, Martin and Paterson, Sarah and Gerig, Guido and Constantino, John and Dager, Stephen and Estes, Annette and Vachet, Clement and Piven, Joseph}, journal={Developmental science}, volume={20}, number={2}, year={2017}, publisher={Wiley Online Library}, comment={ 3D Slicer (www.slicer.org) was used to perform deterministic tractography} } @article{senra2017enhancing, title={Enhancing quality in Diffusion Tensor Imaging with anisotropic anomalous diffusion filter}, author={Senra Filho, Antonio Carlos da Silva and Salmon, Carlos Ernesto Garrido and Santos, Antonio Carlos dos and Junior, Murta and Ot{\'a}vio, Luiz}, journal={Research on Biomedical Engineering}, volume={33}, number={3}, pages={247--258}, year={2017}, publisher={SciELO Brasil}, comment={The tractography reconstructions were made in 3D Slicer software ( Pieper et al., 2004 ; Xia et al., 2008 ), which provides a better control set for image visualization than the FSL tractography toolkit} } @article{hayes2017affective, title={Affective Circuitry Alterations in Patients with Trigeminal Neuralgia}, author={Hayes, Dave J and Chen, David Q and Zhong, Jidan and Lin, Ariel and Behan, Brendan and Walker, Matthew and Hodaie, Mojgan}, journal={Frontiers in neuroanatomy}, volume={11}, pages={73}, year={2017}, publisher={Frontiers}, comment={3D Slicer was used for visualization of diffusion magnetic resonance images (dMRI), seed and ROI drawing, tensor estimation, and the creation of scalar maps for fractional anisotropy (FA), and mean (MD), axial (AD), and radial (RD) diffusivities at the individual level.} } @article{lee2017common, title={Common and heritable components of white matter microstructure predict cognitive function at 1 and 2 y}, author={Lee, Seung Jae and Steiner, Rachel J and Yu, Yang and Short, Sarah J and Neale, Michael C and Styner, Martin Andreas and Zhu, Hongtu and Gilmore, John H}, journal={Proceedings of the National Academy of Sciences}, volume={114}, number={1}, pages={148--153}, year={2017}, publisher={National Acad Sciences}, comment={a total of 12 fiber tract segments consistent with those of Penke et al. (12) were reconstructed using streamline tractography using 3D Slicer (https://www.slicer.org) and defined as follows} } @article{hung2017predicting, title={Predicting pain relief: Use of pre-surgical trigeminal nerve diffusion metrics in trigeminal neuralgia}, author={Hung, Peter S-P and Chen, David Q and Davis, Karen D and Zhong, Jidan and Hodaie, Mojgan}, journal={NeuroImage: Clinical}, year={2017}, publisher={Elsevier}, comment={diffusion-weighted MR images were further processed in 3D Slicer v 4.3.} } @article{levitt2017reduced, title={Reduced structural connectivity in frontostriatal white matter tracts in the associative loop in schizophrenia}, author={Levitt, James J and Nestor, Paul G and Levin, Laura and Pelavin, Paula and Lin, Pan and Kubicki, Marek and McCarley, Robert W and Shenton, Martha E and Rathi, Yogesh}, journal={American Journal of Psychiatry}, volume={174}, number={11}, pages={1102--1111}, year={2017}, publisher={Am Psychiatric Assoc} } @article{joo2017abnormal, title={Abnormal asymmetry of white matter tracts between ventral posterior cingulate cortex and middle temporal gyrus in recent-onset schizophrenia}, author={Joo, Sung Woo and Chon, Myong-Wuk and Rathi, Yogesh and Shenton, Martha E and Kubicki, Marek and Lee, Jungsun}, journal={Schizophrenia Research}, year={2017}, publisher={Elsevier} } @article{rasmussen2017novel, title={A novel maturation index based on neonatal diffusion tensor imaging reflects typical perinatal white matter development in humans}, author={Rasmussen, Jerod M and Kruggel, Frithjof and Gilmore, John H and Styner, Martin and Entringer, Sonja and Consing, Kirsten NZ and Potkin, Steven G and Wadhwa, Pathik D and Buss, Claudia}, journal={International Journal of Developmental Neuroscience}, volume={56}, pages={42--51}, year={2017}, publisher={Elsevier}, comment={Fiber tract streamline DTI tractography (Fillard et al., 2003) was performed via 3D Slicer (version 4.3.0)} } @article{oestreich2017characterizing, title={Characterizing white matter changes in chronic schizophrenia: A free-water imaging multi-site study}, author={Oestreich, Lena KL and Lyall, Amanda E and Pasternak, Ofer and Kikinis, Zora and Newell, Dominick T and Savadjiev, Peter and Bouix, Sylvain and Shenton, Martha E and Kubicki, Marek and Bank, Australian Schizophrenia Research and others}, journal={Schizophrenia Research}, year={2017}, publisher={Elsevier}, comment={All images were masked in order to remove non-brain areas and background noise by manually editing a label map, which was initialized using the OTSU module in the software 3D Slicer (www.slicer.org).} } @article{tuozzo2017patients, title={Patients with chronic bipolar disorder exhibit widespread increases in extracellular free water}, author={Tuozzo, Carissa and Lyall, Amanda E and Pasternak, Ofer and James, Anthony CD and Crow, Timothy J and Kubicki, Marek}, journal={Bipolar disorders}, year={2017}, publisher={Wiley Online Library}, comment={Tensor masks were created for each scan using 3D Slicer software (http://www.slicer.org), followed by manual editing to exclude non-brain areas} } @article{anderson2017optimized, title={Optimized programming algorithm for cylindrical and directional deep brain stimulation electrodes}, author={Anderson, Daria Nesterovich and Osting, Braxton and Vorwerk, Johannes and Dorval, Alan Chuck and Butson, Christopher R}, journal={Journal of neural engineering}, year={2017}, publisher={IOP Publishing}, comment={used a deterministic streamline algorithm in 3D Slicer (Fedorov et al., 2012) to determine fiber trajectories of the IC.} } @article{cherupalli2017magnetic, title={Magnetic Resonance Imaging of the Brain of a Monotreme, the Short-Beaked Echidna (Tachyglossus aculeatus)}, author={Cherupalli, Sandilya and Hardman, Craig D and Bongers, Andre and Ashwell, Ken WS}, journal={Brain, Behavior and Evolution}, year={2017}, publisher={Karger Publishers}, comment={Whole brain fiber tractography was performed on the DTI data sets using the deterministic single-tensor streamline tractography algorithm as implemented in 3DSlicer [Basser et al., 2000]. } } %% added for 2017 with 'Slicer DTI' @article{young2017unc, title={The UNC-Wisconsin Rhesus Macaque Neurodevelopment Database: A Structural MRI and DTI Database of Early Postnatal Development}, author={Young, Jeffrey T and Shi, Yundi and Niethammer, Marc and Grauer, Michael and Coe, Christopher L and Lubach, Gabriele R and Davis, Bradley and Budin, Francois and Knickmeyer, Rebecca C and Alexander, Andrew L and Styner, Martin A.}, journal={Frontiers in neuroscience}, volume={11}, year={2017}, publisher={Frontiers Media SA}, comment={3D Slicer is an open source software package for image visualization and analysis. The converter tool within 3D Slicer computes DWI based on the b-matrix information in the DICOM header.} } @inproceedings{bakhshmand2017real, title={Real-time Interactive Tractography Analysis for Multimodal Brain Visualization Tool: MultiXplore}, author={Bakhshmand, Saeed M and de Ribaupierre, Sandrine and Eagleson, Roy}, booktitle={SPIE Medical Imaging}, pages={101352J--101352J}, year={2017}, organization={International Society for Optics and Photonics}, comment={4 tractography files prepared by 3D Slicer from DTI images} } @inproceedings{chenb2017white, title={White Matter Fiber-based Analysis of T1w/T2w Ratio Map}, author={Chenb, Haiwei and Budine, Francois and Noela, Jean and Prietoa, Juan Carlos and Gilmorea, John and Rasmussenc, Jerod and Wadhwac, Pathik D and Entringerc, Sonja and Bussc, Claudia and Stynera, Martin}, booktitle={SPIE Medical Imaging}, pages={101330P--101330P}, year={2017}, organization={International Society for Optics and Photonics}, comment={fiber tract streamline DTI tractography was performed via 3D slicer (http://www.slicer.org) in the DTI atlas space} } @article{holly2017high, title={High-grade Gliomas Exhibit Higher Peritumoral Fractional Anisotropy and Lower Mean Diffusivity than Intracranial Metastases}, author={Holly, Kevin S and Barker, Benjamin J and Murcia, Derrick and Bennett, Rebekah and Kalakoti, Piyush and Ledbetter, Christina and Gonzalez-Toledo, Eduardo and Nanda, Anil and Sun, Hai}, journal={Frontiers in Surgery}, volume={4}, year={2017}, publisher={Frontiers Media SA}, comment={Using 3D Slicer, FA and MD maps were derived from DTI scans} } @article{jakab2017glioma, title={Glioma Grade Map: A Machine-Learning Based Imaging Biomarker For Tumor Characterization}, author={Jakab, Andras and Molnar, Peter P and Emri, Miklos and Berenyi, Ervin}, journal={bioRxiv}, pages={133249}, year={2017}, publisher={Cold Spring Harbor Labs Journals}, comment={Tumor segmentation, diffusion tensor calculation and coregistrations were executed using the Slicer 3D software package (Pieper et al., 2004), DTI scalar calculations were based on the equations described elsewhere (Basser and Pierpaoli, 1993).} } @article{mayinger2017white, title={White matter alterations in college football players: a longitudinal diffusion tensor imaging study}, author={Mayinger, Michael Christian and Merchant-Borna, Kian and Hufschmidt, Jakob and Muehlmann, Marc and Weir, Isabelle Ruth and Rauchmann, Boris-Stephan and Shenton, Martha Elizabeth and Koerte, Inga Katharina and Bazarian, Jeffrey John}, journal={Brain imaging and behavior}, pages={1--10}, year={2017}, publisher={Springer}, comment={Post-processing of DTI DTI, data sets were visually inspected for image quality using 3D Slicer version 4.3.0 } } @article{wolff2017neural, title={Neural circuitry at age 6 months associated with later repetitive behavior and sensory responsiveness in autism}, author={Wolff, Jason J and Swanson, Meghan R and Elison, Jed T and Gerig, Guido and Pruett, John R and Styner, Martin A and Vachet, Clement and Botteron, Kelly N and Dager, Stephen R and Estes, Annette M and and Hazlett, Heather C. and Schultz, Robert T. and Shen, Mark D. and Zwaigenbaum, Lonnie and Piven, Joseph}, journal={Molecular autism}, volume={8}, number={1}, pages={8}, year={2017}, publisher={BioMed Central}, comment={Deterministic fiber tractography was performed by the first and second author in the study specific, average atlas space using 3D Slicer (https://www.slicer.org/) } } @article{howell2017maternal, title={Maternal buffering beyond glucocorticoids: impact of early life stress on corticolimbic circuits that control infant responses to novelty}, author={Howell, Brittany R and McMurray, Matthew S and Guzman, Dora B and Nair, Govind and Shi, Yundi and McCormack, Kai M and Hu, Xiaoping and Styner, Martin A and Sanchez, Mar M}, journal={Social neuroscience}, volume={12}, number={1}, pages={50--64}, year={2017}, publisher={Taylor \& Francis}, comment={The UF was tracked in each hemisphere using the 3D Slicer software.} } @article{tylee2017machine, title={Machine-learning classification of 22q11. 2 deletion syndrome: A diffusion tensor imaging study}, author={Daniel S. Tylee and Zora Kikinis and Thomas P. Quinn and Kevin M. Antshel and Wanda Fremont and Muhammad A. Tahir and Anni Zhu and Xue Gong and Stephen J. Glatt and Ioana L. Coman and Martha E. Shenton and Wendy R. Kates and Nikos Makris}, journal={NeuroImage: Clinical}, year={2017}, publisher={Elsevier}, comment={ROI connections that significantly discriminated individuals with 22q11.2DS from controls were reconstructed using the image processing program, 3D Slicer, and were visually inspected for the imaging datasets of all study participants by our neuroanatomist (N.M.) and diffusion imaging specialist (Z.K.) These visual inspections served to confirm that the location of these connections corresponded to specific fiber tracts that have been previously described in primate, histological, and diffusion imaging literatures} } @article{shaffer2017longitudinal, title={Longitudinal diffusion changes in prodromal and early HD: Evidence of white-matter tract deterioration}, author={Shaffer, Joseph J and Ghayoor, Ali and Long, Jeffrey D and Kim, Regina Eun-Young and Lourens, Spencer and O'Donnell, Lauren J and Westin, Carl-Fredrik and Rathi, Yogesh and Magnotta, Vincent and Paulsen, Jane S and Johnson, Hans J.}, journal={Human brain mapping}, volume={38}, number={3}, pages={1460--1477}, year={2017}, publisher={Wiley Online Library}, comment={Tractography visualization was performed in 3D Slicer using SlicerDMRI} } @article{zhang2017denoise, title={Denoise Diffusion-Weighted Images Using Higher-Order Singular Value Decomposition}, author={Zhang, Xinyuan and Peng, Jie and Xu, Man and Yang, Wei and Zhang, Zhe and Guo, Hua and Chen, Wufan and Feng, Qianjin and Wu, Ed X and Feng, Yanqiu}, journal={NeuroImage}, year={2017}, publisher={Elsevier}, comment={ shows the reconstructed orientation distribution function (ODF), generated by using the 3DSlicer software (free available at www.slicer.org)} } @article{wassermann2016white, title={The white matter query language: a novel approach for describing human white matter anatomy}, author={Wassermann, Demian and Makris, Nikos and Rathi, Yogesh and Shenton, Martha and Kikinis, Ron and Kubicki, Marek and Westin, Carl-Fredrik}, journal={Brain Structure and Function}, volume={221}, number={9}, pages={4705--4721}, year={2016}, publisher={Springer} } @article{wassermann2010unsupervised, title={Unsupervised white matter fiber clustering and tract probability map generation: Applications of a Gaussian process framework for white matter fibers}, author={Wassermann, Demian and Bloy, Luke and Kanterakis, Efstathios and Verma, Ragini and Deriche, Rachid}, journal={NeuroImage}, volume={51}, number={1}, pages={228--241}, year={2010}, publisher={Elsevier} } @inproceedings{zhang2017automated, title={Automated Connectivity-Based Groupwise Cortical Atlas Generation: Application to Data of Neurosurgical Patients with Brain Tumors for Cortical Parcellation Prediction}, author={Zhang, Fan and Kahali, Pegah and Suter, Yannick and Norton, Isaiah and Rigolo, Laura and Savadjiev, Peter and Song, Yang and Rathi, Yogesh and Cai, Weidong and Wells III, William M. and Golby, Alexandra J. and O'Donnell, Lauren J.}, booktitle={IEEE International Symposium on Biomedical Imaging (ISBI)}, year={2017}, pages={774-777}, organization={IEEE} } @inproceedings{zhang2017comparison, title={Comparison between two white matter segmentation strategies: an investigation into white matter segmentation consistency}, author={Zhang, Fan and Norton, Isaiah and Cai, Weidong and Song, Yang and Wells III, William M. and O'Donnell, Lauren J.}, booktitle={IEEE International Symposium on Biomedical Imaging (ISBI)}, year={2017}, pages={796-799}, organization={IEEE} } %% Keyword 'Slicer DTI' @article{kikinis2017diffusion, title={Diffusion imaging of mild traumatic brain injury in the impact accelerated rodent model: A pilot study}, author={Kikinis, Zora and Muehlmann, Marc and Pasternak, Ofer and Peled, Sharon and Kulkarni, Praveen and Ferris, Craig and Bouix, Sylvain and Rathi, Yogesh and Koerte, Inga K and Pieper, Steve and others}, journal={Brain injury}, volume={31}, number={10}, pages={1376--1381}, year={2017}, publisher={Taylor \& Francis}, comment={Brain masks were generated from the DWI using threshold estimation in 3DSlicer software version 4 (http://www.slicer.org) [24]} } @article{nishioka2017disease, title={Disease stage-dependent relationship between diffusion tensor imaging and electrophysiology of the visual system in a murine model of multiple sclerosis}, author={Nishioka, Christopher and Liang, Hsiao-Fang and Chung, Chen-Fang and Sun, Shu-Wei}, journal={Neuroradiology}, volume={59}, number={12}, pages={1241--1250}, year={2017}, publisher={Springer}, comment={Corrected scans were then imported into 3D Slicer, where eigenvalues derived from the diffusion tensor were} } @article{yamada2017diffusion, title={Diffusion tensor imaging evaluation of neural network development in patients undergoing therapeutic repetitive transcranial magnetic stimulation following stroke}, author={Yamada, Naoki and Ueda, R and Kakuda, W and Momosaki, R and Kondo, T and Hara, T and Senoo, A and Abo, M}, journal={Brain Stimulation}, volume={2}, number={10}, pages={509}, year={2017}, publisher={Elsevier}, comment={We loaded each BA into 3D slicer and displayed the corpus callosum and corticospinal tract as indicated in Figure 1.} } %% added by Lauren Jan 2017 % query: "slicer neurosurgery diffusion" (only did a few from 2016 so far) @article{song2016vivo, title={In vivo visualization of the facial nerve in patients with acoustic neuroma using diffusion tensor imaging--based fiber tracking}, author={Song, Fei and Hou, Yuanzheng and Sun, Guochen and Chen, Xiaolei and Xu, Bainan and Huang, Jason H and Zhang, Jun}, journal={Journal of neurosurgery}, volume={125}, number={4}, pages={787--794}, year={2016}, publisher={American Association of Neurological Surgeons}, comment={ The visualized FN course and its position relative to the tumors were determined using DTI-FT with 3D Slicer software. } } %% end added by Lauren Jan 2017 @article{nestor2007attentional, title={Attentional networks and cingulum bundle in chronic schizophrenia}, author={Nestor, Paul G and Kubicki, Marek and Spencer, Kevin M and Niznikiewicz, Margaret and McCarley, Robert W and Shenton, Martha E}, journal={Schizophrenia research}, volume={90}, number={1}, pages={308--315}, year={2007}, publisher={Elsevier}, comment={directional diffusion maps were generated using in-house software (www.slicer.org).} } @inproceedings{oubel2009evaluation, title={Evaluation of Different Strategies for Distortion Correction in Fetal Diffusion-Weighted Imaging}, author={Oubel, Estanislao and Rousseau, Francois and Noblet, Vincent and Koob, Meriam and Armspach, Jean-Paul and Dietemann, Jean-Louis}, booktitle={MICCAI workshop: image analysis for the developing brain. London, UK}, year={2009}, pages={0}, comment={Slicer (http://www.slicer.org) was employed for tensor estimation and the cal- culation of scalar indexes.} } @article{kim2015white, title={White matter alterations are associated with suicide attempt in patients with panic disorder}, author={Kim, Borah and Oh, Jongsoo and Kim, Min-Kyoung and Lee, Sungjae and Tae, Woo Suk and Kim, Chan Mo and Choi, Tai Kiu and Lee, Sang-Hyuk}, journal={Journal of affective disorders}, volume={175}, pages={139--146}, year={2015}, publisher={Elsevier}, comment={whole brain FA skeleton as well as its components were calculated using 3D-slicer (v3.6.3, http://www.slicer.org).} } @article{nishioka2015diffusion, title={Diffusion tensor imaging reveals visual pathway damage in patients with mild cognitive impairment and Alzheimer's disease}, author={Nishioka, Christopher and Poh, Christina and Sun, Shu-Wei}, journal={Journal of Alzheimer's Disease}, volume={45}, number={1}, pages={97--107}, year={2015}, publisher={IOS Press}, comment={Maps for five DTI indices, including FA, trace diffusion (TR), axial (?II), radial (?[perpendicular]) diffusivity and eigen3 (?3) were generated using 3D slicer [17, 19].} } @book{liu2015content, title={Content-based retrieval of brain diffusion magnetic resonance image}, author={Liu, Siqi and Hadi, Nur and Liu, Sidong and Pujol, Sonia and Kikinis, Ron and Zhang, Fan and Feng, Dagan and Cai, Weidong}, booktitle={Multimodal Retrieval in the Medical Domain}, pages={54--60}, year={2015}, comment={An example FA index slice which represents the mean water diffusivity within a voxel rendered with 3D Slicer 4.4}, publisher={Springer} } @inproceedings{mostapha2015novel, title={A novel framework for the segmentationof mrinfant brain images}, author={Mostapha, Mahmoud and Casanova, Manuel F and El-Baz, Ayman}, booktitle={IEEE International Conference on Image Processing (ICIP), }, pages={88--92}, year={2015}, organization={IEEE}, url={http://ieeexplore.ieee.org/document/7350765/}, comment={Derive DTI from DWI using the weighted linear least square (WLLS) method, and extract five DTI anisotropy features (MD, FA, RA, ? , ??) using 3D Slicer [14].} } @article{mora2015application, title={The Application of DTI to Investigate Abnormalities in Schizophrenia and Alzheimer Disease.}, author={Mora, Martha L and Hurtado, Carlos A and Prchkovska, Vesna and Rodrigues, Paulo and L{\'o}pez, Juan Jos{\'e}}, journal={Biomedical Research}, volume={26}, number={4}, pages={621--624}, year={2015}, comment={the diffusion tensor was estimated for each voxel, by means of weighted with method least-squares in 3D Slicer programming} } @article{howell2016maternal, title={Maternal buffering beyond glucocorticoids: impact of early life stress on corticolimbic circuits that control infant responses to novelty}, author={Howell, Brittany R and McMurray, Matthew S and Guzman, Dora B and Nair, Govind and Shi, Yundi and McCormack, Kai M and Hu, Xiaoping and Styner, Martin A and Sanchez, Mar M}, journal={Social neuroscience}, pages={1--15}, year={2016}, publisher={Taylor \& Francis}, url={http://www.tandfonline.com/doi/abs/10.1080/17470919.2016.1200481}, comment={The UF was tracked in each hemisphere using the 3D Slicer software (Figure 2)} } @article{wang2016mapping, title={Mapping 3D fiber orientation in tissue using dual-angle optical polarization tractography}, author={Wang, Y and Ravanfar, M and Zhang, K and Duan, D and Yao, G}, journal={Biomedical Optics Express}, volume={7}, number={10}, pages={3855--3870}, year={2016}, publisher={Optical Society of America}, url={https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-10-3855}, comment={The 3DSlicer software (www.slicer.org) was used for visualizing the 3D OPT (Optical polarization tractography) results.}, } @article{savadjiev2016sexual, title={Sexual dimorphic abnormalities in white matter geometry common to schizophrenia and non-psychotic high-risk subjects: Evidence for a neurodevelopmental risk marker?}, author={Savadjiev, Peter and Seidman, Larry J and Thermenos, Heidi and Keshavan, Matcheri and Whitfield-Gabrieli, Susan and Crow, Tim J and Kubicki, Marek}, journal={Human brain mapping}, volume={37}, number={1}, pages={254--261}, year={2016}, url={http://onlinelibrary.wiley.com/doi/10.1002/hbm.23026/full}, publisher={Wiley Online Library}, comment={ Tensors were estimated using the Least Squares method [Tristán-Vega et al., 2012] and the 3DSlicer software version 3.6.4 (www.slicer.org).} } @article{magtibay2016feature, title={Feature-based MRI data fusion for cardiac arrhythmia studies}, author={Magtibay, Karl and Beheshti, Mohammadali and Foomany, Farbod Hosseyndoust and Masse, Stephane and Lai, Patrick FH and Zamiri, Nima and Asta, John and Nanthakumar, Kumaraswamy and Jaffray, David and Krishnan, Sridhar and Umapathy, Karthikeyan}, journal={Computers in biology and medicine}, volume={72}, pages={13--21}, year={2016}, comment={To calculate diffusion tensor images, an open-source program, 3D slicer [34], was used.}, publisher={Elsevier} } @article{beheshti2016modeling, title={Modeling Current Density Maps Using Aliev--Panfilov Electrophysiological Heart Model}, author={Beheshti, M and Foomany, FH and Magtibay, K and Masse, S and Lai, P and Asta, J and Jaffray, DA and Nanthakumar, K and Krishnan, S and Umapathy, K}, journal={Cardiovascular Engineering and Technology}, volume={7}, number={3}, pages={238--253}, year={2016}, publisher={Springer}, comment={The diffusion weighted images obtained from the GE machine were reconstructed into directionally color coded diffusion tensor images using 3D Slicer software} } @article{willi2016characterization, title={Characterization of white matter integrity deficits in cocaine-dependent individuals with substance-induced psychosis compared with non-psychotic cocaine users}, author={Willi, Taylor S. and Barr, Alasdair M. and Gicas, Kristina and Lang, Donna J. and Vila-Rodriguez, Fidel and Su, Wayne and Thornton, Allen E. and Leonova, Olga and Giesbrecht, Chantelle J. and Procyshyn, Ric M. and Rauscher, Alexander and MacEwan, William G. and Honer, William G. and Panenka, William J.}, journal={Addiction biology}, year={2016}, publisher={Wiley Online Library}, comment={DTI fitting was performed with Slicer 3 using non-linear least-square fitting with shifted negative eigenvalues.} } @article{rasmussen2016novel, title={A Novel Maturation Index Based on Neonatal Diffusion Tensor Imaging Reflects Typical Perinatal White Matter Development in Humans}, author={Rasmussen, Jerod M and Kruggel, Frithjof and Gilmore, John H and Styner, Martin and Entringer, Sonja and Consing, Kirsten NZ and Potkin, Steven G and Wadhwa, Pathik D and Buss, Claudia}, journal={International Journal of Developmental Neuroscience}, year={2016}, publisher={Elsevier}, url={http://www.sciencedirect.com/science/article/pii/S0736574816302283}, comment={Fiber tract streamline DTI tractography (Fillard et al., 2003) was performed via 3D Slicer (version 4.3.0) (http://www.slicer.org) in the DTI atlas space followed by fiber cleaning with FiberVie.} } @article{odonnell2016automated, title={Automated White Matter Fiber Tract Identification in Patients with Brain Tumors}, author={O'Donnell, Lauren J and Suter, Yannick and Rigolo, Laura and Kahali, Pegah and Zhang, Fan and Norton, Isaiah and Albi, Angela and Olubiyi, Olutayo and Meola, Antonio and Essayed, Walid I and Unadkat, Prashin and Ciris, Pelin Aksit and Wells III, William M. and Rathi, Yogesh and Westin, Carl-Fredrik and Golby, Alexandra J.}, journal={NeuroImage: Clinical}, year={2016}, volume={13}, pages={138 - 153}, url={http://www.sciencedirect.com/science/article/pii/S2213158216302315}, publisher={Elsevier} } @phdthesis{odonnell2006cerebral, title={Cerebral White Matter Analysis Using Diffusion Imaging}, author={O'Donnell, Lauren J.}, year={2006}, school={Massachusetts Institute of Technology} } @phdthesis{ziyan2006population, title={Population-wise consistent segmentation of diffusion weighted magnetic resonance images}, author={Ziyan, Ulas}, year={2008}, school={Massachusetts Institute of Technology} } @article{krishna2016diffusion, title={Diffusion tensor imaging assessment of microstructural brainstem integrity in Chiari malformation Type I}, author={Krishna, Vibhor and Sammartino, Francesco and Yee, Philip and Mikulis, David and Walker, Matthew and Elias, Gavin and Hodaie, Mojgan}, journal={Journal of neurosurgery}, volume={125}, number={50}, pages={1112-1119}, year={2016}, publisher={American Association of Neurological Surgeons} } @article{makris2016mapping, title={Mapping temporo-parietal and temporo-occipital cortico-cortical connections of the human middle longitudinal fascicle in subject-specific, probabilistic, and stereotaxic Talairach spaces}, author={Makris, Nikos and Zhu, A and Papadimitriou, GM and Mouradian, P and Ng, I and Scaccianoce, E and Baselli, G and Baglio, F and Shenton, ME and Rathi, Y and Dickerson, B. and Yeterian, E. and Kubicki, M.}, journal={Brain Imaging and Behavior}, volume={NA}, number={NA}, pages={1--20}, year={2016}, publisher={Springer}, comment={Tractographic delineation of MdLF HARDI tractography was performed in 3D-Slicer (v2.7, www.slicer.org), using a multi-tensor tractography algorithm (Malcolm et al. 2010). } } @article {albi2017free, author = {Albi, Angela and Pasternak, Ofer and Minati, Ludovico and Marizzoni, Moira and Bartr{\'e}s-Faz, David and Bargall{\'o}, N{\'u}ria and Bosch, Beatriz and Rossini, Paolo Maria and Marra, Camillo and M{\"u}ller, Bernhard and others}, title = {Free water elimination improves test?retest reproducibility of diffusion tensor imaging indices in the brain: A longitudinal multisite study of healthy elderly subjects}, journal = {Human Brain Mapping}, volume = {38}, number = {1}, url = {http://dx.doi.org/10.1002/hbm.23350}, pages = {12--26}, keywords = {multisite diffusion MRI, free-water imaging, test?retest reproducibility, brain diffusion tensor imaging, longitudinal, healthy elderly}, year = {2017}, comment={DTI analysis was performed by the least squares method, estimating a tensor for each image voxel (Basser and Jones, 2002), using the ?Diffusion Tensor Estimation? module in 3D Slicer (https://www.slicer.org).} } @article{tong2016view, title={View-Dependent Streamline Deformation and Exploration}, author={Tong, Xin and Edwards, John and Chen, Chun-Ming and Shen, Han-Wei and Johnson, Chris R and Wong, Pak Chung}, journal={IEEE transactions on visualization and computer graphics}, volume={22}, number={7}, url={http://ieeexplore.ieee.org/document/7332955/}, pages={1788--1801}, year={2016}, publisher={IEEE}, comment={ To demonstrate the use of our layered lenses, we apply it on white matter tracts which are generated from a brain diffu- sion tensor dataset using the 3D Slicer software [30], [31].} } @article{wang2016development, title={Development of Tract-Specific White Matter Pathways During Early Reading Development in At-Risk Children and Typical Controls}, author={Wang, Yingying and Mauer, Meaghan V and Raney, Talia and Peysakhovich, Barbara and Becker, Bryce LC and Sliva, Danielle D and Gaab, Nadine}, journal={Cerebral Cortex}, volume={25}, number={11}, pages={1-17}, year={2016}, publisher={Oxford Univ Press}, comment={DWI DICOM data were converted into NRRD (teem.sourceforge.net/nrrd/) format using DicomToNrrdConverter software from Slicer4 (www.slicer.org).} } @article{young2016brain, title={Brain-Computer Interface Training after Stroke Affects Patterns of Brain--Behavior Relationships in Corticospinal Motor Fibers}, author={Young, Brittany M. and Stamm, Julie M. and Song, Jie and Remsik, Alexander B. and Nair, Veena A. and Tyler, Mitchell E. and Edwards, Dorothy F. and Caldera, Kristin and Sattin, Justin A. and Williams, Justin C. and Prabhakaran, Vivek}, journal={Frontiers in Human Neuroscience}, volume={10}, year={2016}, pages={457}, publisher={Frontiers Media SA}, comment={Deterministic tractography was performed using 3D Slicer with a fractional anisotropy (FA) threshold of 0.15 (Mori and van Zijl, 2002; Stamm et al., 2015) with tracts originating from each PLIC ROI.} } @article{lee2016white, title={White matter alterations associated with suicide in patients with schizophrenia or schizophreniform disorder}, author={Lee, Sung-Jae and Kim, Borah and Oh, Daeyoung and Kim, Min-Kyoung and Kim, Keun-Hyang and Bang, Seong Yun and Choi, Tai Kiu and Lee, Sang-Hyuk}, journal={Psychiatry Research: Neuroimaging}, volume={248}, pages={23--29}, year={2016}, publisher={Elsevier}, comment={Then, mean FAs of the difference in the two groups of brain FA skeleton, as well as its components were calculated using 3D-slicer (v3.6.3, http://www.slicer.org).} } @article{przybyszewski2016multi, title={Multi-parametric analysis assists in STN localization in Parkinson's patients}, author={Przybyszewski, AW and Ravin, P and Pilitsis, JG and Szymanski, A and Barborica, A and Novak, P}, journal={Journal of the Neurological Sciences}, volume={366}, pages={37--43}, year={2016}, publisher={Elsevier}, comment={By using the Tractography Interactive Seeding module (3D Slicer) a tract was generated for this particular ROI } } @inproceedings{goh2016patient, title={Patient-tailored multimodal neuroimaging, visualization and quantification of human intra-cerebral hemorrhage}, author={Goh, Sheng-Yang M and Irimia, Andrei and Vespa, Paul M and Van Horn, John D}, booktitle={SPIE Medical Imaging}, pages={978903--978903}, year={2016}, organization={International Society for Optics and Photonics}, comment={These tracts are subsequently loaded and viewed in 3D Slicer.} } @article{fischer2016right, title={Right inferior longitudinal fasciculus lesions disrupt visual-emotional integration}, author={Fischer, David B. and Perez, David L. and Prasad, Sashank and Rigolo, Laura and O'Donnell, Lauren J. and Acar, Diler and Meadows, Mary-Ellen and Baslet, Gaston and Boes, Aaron D. and Golby, Alexandra J. and Dworetzky, Barbara A.}, journal={Social cognitive and affective neuroscience}, volume={11}, number={6}, pages={945--951}, year={2016}, publisher={Oxford University Press}, comment={ Whole brain single tensor unscented Kalman filter tractography (Malcolm et al., 2009) was performed followed by tract selection in 3D Slicer 4.4 (http://www.slicer.org).} } @article{oestreich2016abnormal, title={Abnormal white matter microstructure and increased extracellular free-water in the cingulum bundle associated with delusions in chronic schizophrenia}, author={Oestreich, Lena KL and Pasternak, Ofer and Shenton, Martha E and Kubicki, Marek and Gong, Xue and Bank, Australian Schizophrenia Research and McCarthy-Jones, Simon and Whitford, Thomas J}, journal={NeuroImage: Clinical}, volume={12}, pages={405--414}, year={2016}, publisher={Elsevier}, comment={Diffusion tensor tractography. The cingulum bundle, fornix and uncinate fasciculus were extracted with deterministic (streamline) tractography using 3D Slicer software (see Fig. 1).} } @article{mormina2016optic, title={Optic radiations evaluation in patients affected by high-grade gliomas: a side-by-side constrained spherical deconvolution and diffusion tensor imaging study}, author={Mormina, Enricomaria and Arrigo, Alessandro and Calamuneri, Alessandro and Alafaci, Concetta and Tomasello, Francesco and Morabito, Rosa and Marino, Silvia and Longo, Marcello and Vinci, Sergio Lucio and Granata, Francesca}, journal={Neuroradiology}, volume={58}, number={11}, pages={1067?1075}, year={2016}, publisher={Springer}, comment={Latter data were then loaded into 3DSlicer software (www.slicer.org) [13], together with co-registered T1-weighted images overlaid, to visualize 3D spatial relationship between OR tracts and neoplasm-segmented ROI.} } @inproceedings{zhang2016fiber, title={Fiber clustering based white matter connectivity analysis for prediction of Autism Spectrum Disorder using diffusion tensor imaging}, author={Zhang, Fan and Savadjiev, Peter and Cai, Weidong and Song, Yang and Verma, Ragini and Westin, Carl-Fredrik and O'Donnell, Lauren J}, booktitle={IEEE International Symposium on Biomedical Imaging (ISBI)}, pages={564--567}, year={2016}, organization={IEEE} } @article{bergden2016development, title={Development of a 3D Interactive Model for Teaching Intercortical Connectivity of Cerebral White Matter Tracts}, author={Bergden, Jessica and Stabio, Maureen Estevez}, journal={The FASEB Journal}, volume={30}, number={1 Supplement}, pages={568--19}, year={2016}, publisher={FASEB}, comment={3D Slicer was used to estimate the position and direction of fiber tracts and to generate a preliminary tractography model based on fractional anisotropy values. } } @article{ma2016preoperative, title={Preoperative Visualization of Cranial Nerves in Skull Base Tumor Surgery Using Diffusion Tensor Imaging Technology}, author={Ma, JUN and Shaobo, Su and Shuyuan, Yue and Zhao, YAN and Yonggang, Li and Xiaochen, Chen and Ma, HUI}, journal={Turk Neurosurg}, volume={26}, number={6}, pages={805-812}, year={2016}, comment={With special parameters, DTI combined with 3D slicer software to achieve tractography in our study. } } @article{seitz2016tractography, title={Tractography Analysis of 5 White Matter Bundles and Their Clinical and Cognitive Correlates in Early-Course Schizophrenia}, author={Seitz, Johanna and Zuo, Jessica X. and Lyall, Amanda E. and Makris, Nikos and Kikinis, Zora and Bouix, Sylvain and Pasternak, Ofer and Fredman, Eli and Duskin, Jonathan and Goldstein, Jill M. and Petryshen, Tracey L. and Mesholam-Gately, Raquelle I. and Wojcik, Joanne and McCarley, Robert W. and Seidman, Larry J. and Shenton, Martha E. and Koerte, Inga K. and Kubicki, Marek}, journal={Schizophrenia bulletin}, volume={42}, number={3}, pages={762--771}, year={2016}, publisher={MPRC}, comment={The resulting corrected images were then input into 3D slicer (www.slicer.org, accessed November 19, 2015), which was used for weighted least square tensor estimation followed by human expert supervised streamline tractography (neuroanatomist NM). } } @article{shany2016diffusion, title={Diffusion Tensor Tractography of the Cerebellar Peduncles in Prematurely Born 7-Year-Old Children}, author={Shany, Eilon and Inder, Terrie E and Goshen, Sharon and Lee, Iris and Neil, Jeffrey J and Smyser, Christopher D and Doyle, Lex W and Anderson, Peter J and Shimony, Joshua S}, journal={The Cerebellum}, pages={1--12}, volume={0}, number={0}, year={2016}, publisher={Springer}, comment={Full brain tractography was filtered using regions of interest (ROIs) manually placed perpendicular to the length of the tract based on anatomical landmarks in native space using Analyze 10 (Mayo Clinic, Rochester MN) and visualized on Slicer 2.5 (http://www.slicer.org/).} } @article{chen2016corticospinal, title={Corticospinal tract modeling for neurosurgical planning by tracking through regions of peritumoral edema and crossing fibers using two-tensor unscented Kalman filter tractography}, author={Chen, Zhenrui and Tie, Yanmei and Olubiyi, Olutayo and Zhang, Fan and Mehrtash, Alireza and Rigolo, Laura and Kahali, Pegah and Norton, Isaiah and Pasternak, Ofer and Rathi, Yogesh and Golby, Alexandra J. and O'Donnell, Lauren J.}, journal={International journal of computer assisted radiology and surgery}, volume={11}, number={8}, pages={1475?1486}, year={2016}, publisher={Springer} } @ARTICLE{zhong2016an, AUTHOR={Zhong, Jidan and Chen, David Q. and Walker, Matthew and Waspe, Adam and Looi, Thomas and Piorkowska, Karolina and Drake, James M. and Hodaie, Mojgan}, TITLE={An In vivo Multi-Modal Structural Template for Neonatal Piglets Using High Angular Resolution and Population-Based Whole-Brain Tractography}, JOURNAL={Frontiers in Neuroanatomy}, VOLUME={10}, PAGES={92}, YEAR={2016}, comment={3D Slicer was used to extract the fibers passing through specific fibers.} } @article{fuster2016adjugate, title={Adjugate diffusion tensors for geodesic tractography in white matter}, author={Fuster, Andrea and Haije, Tom Dela and Tristan-Vega, Antonio and Plantinga, Birgit and Westin, Carl-Fredrik and Florack, Luc}, journal={Journal of Mathematical Imaging and Vision}, volume={54}, number={1}, pages={1-14}, year={2016}, publisher={Springer}, url={http://link.springer.com/article/10.1007/s10851-015-0586-8}, comment={We visualize the obtained tracts using 3D Slicer} } @inproceedings{yao2016optical, title={Optical polarization tractography based on polarization-sensitive optical coherence tomography}, author={Yao, Gang and Wang, Yuanbo and Ravanfar, Mohammadreza and Azinfar, Leila and Yao, Xuan and Zhang, Keqing and Duan, Dongsheng}, booktitle={SPIE BiOS}, pages={969716-969716}, year={2016}, organization={International Society for Optics and Photonics}, comment={For efficient visualization, the 3D tractographic rendering of the fiber orientation data can be performed using the 3D Slice software (www.slicer.org)} } @article{pujol2015dti, title={The DTI challenge: toward standardized evaluation of diffusion tensor imaging tractography for neurosurgery}, author={Pujol, Sonia and Wells, William and Pierpaoli, Carlo and Brun, Caroline and Gee, James and Cheng, Guang and Vemuri, Baba and Commowick, Olivier and Prima, Sylvain and Stamm, Aymeric and others}, journal={Journal of Neuroimaging}, volume={25}, number={6}, pages={875--882}, year={2015}, publisher={Wiley Online Library} } @article{chen2015reconstruction, title={Reconstruction of the arcuate fasciculus for surgical planning in the setting of peritumoral edema using two-tensor unscented Kalman filter tractography}, author={Chen, Zhenrui and Tie, Yanmei and Olubiyi, Olutayo and Rigolo, Laura and Mehrtash, Alireza and Norton, Isaiah and Pasternak, Ofer and Rathi, Yogesh and Golby, Alexandra J and O'Donnell, Lauren J}, journal={NeuroImage: Clinical}, volume={7}, pages={815--822}, year={2015}, publisher={Elsevier} } @article{hayes2015subcallosal, title={Subcallosal cingulate connectivity in anorexia nervosa patients differs from healthy controls: a multi-tensor tractography study}, author={Hayes, Dave J and Lipsman, Nir and Chen, David Q and Woodside, D Blake and Davis, Karen D and Lozano, Andres M and Hodaie, Mojgan}, journal={Brain stimulation}, volume={8}, number={4}, pages={758--768}, year={2015}, publisher={Elsevier}, comment={The eXtended Streamline Tractography, or XST, algorithm was used for whole-brain deterministic multi-tensor tractography (MTT) implemented in 3D Slicer software.} } @article{radmanesh2015comparison, title={Comparison of seeding methods for visualization of the corticospinal tracts using single tensor tractography}, author={Radmanesh, Alireza and Zamani, Amir A and Whalen, Stephen and Tie, Yanmei and Suarez, Ralph O and Golby, Alexandra J}, journal={Clinical neurology and neurosurgery}, volume={129}, pages={44--49}, year={2015}, publisher={Elsevier}, comment={We used open-source publicly available software 3D-slicer version 3.6 in all cases to calculate the tensor and to seed and delineate the 3D fiber tracts with a 1-mm seedpoint grid. } } @article{mormina2015mri, title={MRI tractography of corticospinal tract and arcuate fasciculus in high-grade gliomas performed by constrained spherical deconvolution: qualitative and quantitative analysis}, author={Mormina, E and Longo, M and Arrigo, A and Alafaci, C and Tomasello, F and Calamuneri, A and Marino, S and Gaeta, M and Vinci, SL and Granata, F}, journal={American Journal of Neuroradiology}, volume={36}, number={10}, pages={1853--1858}, year={2015}, publisher={Am Soc Neuroradiology}, comment={the 3D visualization of tracts were performed by using 3D Slicer software (www.slicer.org)} } @article{whitford2015cingulum, title={Cingulum bundle integrity associated with delusions of control in schizophrenia: preliminary evidence from diffusion-tensor tractography}, author={Whitford, Thomas J and Kubicki, Marek and Pelavin, Paula E and Lucia, Diandra and Schneiderman, Jason S and Pantelis, Christos and McCarley, Robert W and Shenton, Martha E}, journal={Schizophrenia research}, volume={161}, number={1}, pages={36--41}, year={2015}, publisher={Elsevier}, comment={All image analysis was performed with the 3D-Slicer software package (http://www.slicer.org, Surgical Planning Laboratory ... superior longitudinal fasciculus (SLF), arcuate fasciculus, and cingulum bundle, were extracted from the DTIs with deterministic (streamline) tractography.} } @article{makris2015variability, title={Variability and anatomical specificity of the orbitofrontothalamic fibers of passage in the ventral capsule/ventral striatum (VC/VS): precision care for patient-specific tractography-guided targeting of deep brain stimulation (DBS) in obsessive compulsive disorder (OCD)}, author={Makris, Nikolaos and Rathi, Yogesh and Mouradian, Palig and Bonmassar, Giorgio and Papadimitriou, George and Ing, Wingkwai I and Yeterian, Edward H and Kubicki, Marek and Eskandar, Emad N and Wald, Lawrence L and Fan, Qiuyun and Nummenmaa, Aapo and Widge, Alik S. and Dougherty, Darin D.}, journal={Brain imaging and behavior}, volume={10}, number={4}, pages={1054?1067}, year={2016}, publisher={Springer}, comment={Fiber tracts were sampled in 3D- Slicer (v2.7, www.slicer.org), using a multi ... Tractographic delineation of lateral and medial orbitofrontothalamic (lOFC-thal and mOFC-thal) fiber tracts Fiber tractography was performed using a multi-tensor tractography algorithm} } @article{kikinis2015anterior, title={Anterior commissural white matter fiber abnormalities in first-episode psychosis: A tractography study}, author={Kikinis, Zora and Fitzsimmons, Jennifer and Dunn, Chandler and Vu, Mai-Anh and Makris, Nikos and Bouix, Sylvain and Goldstein, Jill M and Mesholam-Gately, Raquelle I and Petryshen, Tracey and del Re, Elisabetta C and Wojcik, Joanne and Seidman, Larry J. and Kubicki, Marek}, journal={Schizophrenia research}, volume={162}, number={1-3}, pages={29--34}, year={2015}, publisher={Elsevier}, comment={Tensors were estimated by the least squares method (Basser and Jones, 2002) using 3DSlicer software version 3.6.2 version (http://www.slicer.org/) } } @book{farhat2015role, title={Role of Computers and Image Processing in Image-Guided Brain Tumor Surgery}, author={Farhat, Nabgha and Kapur, Tina and Kikinis, Ron}, booktitle={Image-Guided Neurosurgery}, editor={Alexandra J. Golby}, pages={143--160}, year={2015}, chapte={6}, publisher={Elsevier} } @article{chen2015diffusivity, title={Diffusivity signatures characterize trigeminal neuralgia associated with multiple sclerosis}, author={Chen, David Q and DeSouza, Danielle D and Hayes, David J and Davis, Karen D and O'Connor, Paul and Hodaie, Mojgan}, journal={Multiple Sclerosis Journal}, volume={22}, number={1}, pages={51-63}, year={2015}, publisher={SAGE Publications}, comment={imported into 3D Slicer for single-tensor diffusion tractography (SDT), } } @article{mccarthy2015reduced, title={Reduced integrity of the left arcuate fasciculus is specifically associated with auditory verbal hallucinations in schizophrenia}, author={McCarthy-Jones, Simon and Oestreich, Lena KL and Bank, Australian Schizophrenia Research and Whitford, Thomas J}, journal={Schizophrenia research}, volume={162}, number={1}, pages={1--6}, year={2015}, publisher={Elsevier}, comment={The AF L was extracted from DT images using deterministic tractography (as per Whitford et al., 2011) and implemented in the Slicer-3 software package (version 4.2.0, nightly build, www.slicer.org)} } @article{stamm2015age, title={Age at first exposure to football is associated with altered corpus callosum white matter microstructure in former professional football players}, author={Stamm, Julie M and Koerte, Inga K and Muehlmann, Marc and Pasternak, Ofer and Bourlas, Alexandra P and Baugh, Christine M and Giwerc, Michelle Y and Zhu, Anni and Coleman, Michael J and Bouix, Sylvain and Fritts, Nathan G. and and Martin, Brett M. and Chaisson, Christine and McClean, Michael D. and Lin, Alexander P. and Cantu, Robert C. and Tripodis, Yorghos and Stern, Robert A. and Shenton, Martha E.}, journal={Journal of neurotrauma}, volume={32}, number={22}, pages={1768--1776}, year={2015}, publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}, comment={Seeding of fiber tracts through the whole CC and CC subregions was conducted in 3D Slicer using a deterministic (streamline) tractography approach,} } @article{oestreich2015decreased, title={Decreased integrity of the fronto-temporal fibers of the left inferior occipito-frontal fasciculus associated with auditory verbal hallucinations in schizophrenia}, author={Oestreich, Lena KL and McCarthy-Jones, Simon and Australian Schizophrenia Research Bank and Whitford, Thomas J}, journal={Brain imaging and behavior}, volume={10}, number={2}, pages={445?454}, year={2015}, publisher={Springer}, comment={ A streamline tractography method, using Slicer 3D software (version 4.2.0, www.slicer.org) was adopted for extracting the IOFF} } @article{swanson2015splenium, title={Splenium development and early spoken language in human infants}, author={Swanson, Meghan R. and Wolff, Jason J. and Elison, Jed T. and Gu, Hongbin and Hazlett, Heather C. and Botteron, Kelly and Styner, Martin and Paterson, Sarah and Gerig, Guido and Constantino, John and Dager, Stephen and Estes, Annette and Vachet, Clement and Piven, Joseph and the IBIS Network}, journal={Developmental science}, volume={NA}, number={NA}, pages={NA}, year={2015}, publisher={Wiley Online Library}, comment={3D Slicer (www.slicer.org) was used to perform deterministic tractography.} } @article{o2015does, title={Does diffusion MRI tell us anything about the white matter? An overview of methods and pitfalls}, author={O'Donnell, Lauren J and Pasternak, Ofer}, journal={Schizophrenia research}, volume={161}, number={1}, pages={133--141}, year={2015}, publisher={Elsevier} } @article{chen2015age, title={Age-related changes in diffusion tensor imaging metrics of fornix subregions in healthy humans}, author={Chen, David Qixiang and Strauss, Ido and Hayes, Dave J and Davis, Karen D and Hodaie, Mojgan}, journal={Stereotactic and functional neurosurgery}, volume={93}, number={3}, pages={151--159}, year={2015}, publisher={Karger Publishers}, comment={All image processing and tractography analyses were completed using 3D Slicer software [30].} } @article{lee2015quantitative, title={Quantitative tract-based white matter heritability in twin neonates}, author={Lee, Seung Jae and Steiner, Rachel J and Luo, Shikai and Neale, Michael C and Styner, Martin and Zhu, Hongtu and Gilmore, John H}, journal={NeuroImage}, volume={111}, pages={123--135}, year={2015}, publisher={Elsevier}, comment={all fiber tract segments were reconstructed in the neonate atlas space using a streamline tractography algorithm (www.slicer.org; Fedorov et al., 2012), } } @article{duncan2015negative, title={Negative childhood experiences alter a prefrontal-insular-motor cortical network in healthy adults: A preliminary multimodal rsfMRI-fMRI-MRS-dMRI study}, author={Duncan, Niall W. and Hayes, Dave J. and Wiebking, Christine and Tiret, Brice and Pietruska, Karin and Chen, David Q. and Rainville, Pierre and Marja?ska, Ma?gorzata and Ayad, Omar and Doyon, Julien and Hodaie, Mojgan and Northoff, Georg}, journal={Human brain mapping}, volume={36}, number={11}, pages={4622--4637}, year={2015}, publisher={Wiley Online Library}, comment={Whole-brain deterministic multitensor tractography was performed using the eXtended Streamline Tractography, or XST, algorithm implemented in 3D Slicer [Qazi et al., 2009]} } @inproceedings{mostapha2015towards, title={Towards Non-invasive Image-Based Early Diagnosis of Autism}, author={Mostapha, M and Casanova, MF and Gimelfarb, G and El-Baz, A}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={160--168}, year={2015}, comment={In this paper, the obtained WM label maps were used as seeds to generate the required WM tracts according to existing tractography methods built in the 3D slicer software} } @article{de2015attention, title={Attention deficit/hyperactivity disorder and medication with stimulants in young children: a DTI study}, author={de Luis-Garc{\'\i}a, Rodrigo and Cab{\'u}s-Pi{\~n}ol, Gemma and Imaz-Roncero, Carlos and Argibay-Qui{\~n}ones, Daniel and Barrio-Arranz, Gonzalo and Aja-Fern{\'a}ndez, Santiago and Alberola-L{\'o}pez, Carlos}, journal={Progress in Neuro-Psychopharmacology and Biological Psychiatry}, volume={57}, pages={176--184}, year={2015}, publisher={Elsevier}, comment={With regard to GTS analysis, whole-brain deterministic tractography was performed on the tensor volume using Slicer 3.6 (http://www.slicer.org),} } @article{szymanski2015data, title={Data mining and neural network simulations can help to improve deep brain stimulation effects in Parkinson's disease}, author={Szyma?ski, A and Kubis, Anna and Przybyszewski, Andrzej W}, journal={Computer Science}, volume={16}, number={2}, pages={199}, year={2015}, comment={After postoperative to preoperative images were registered, we transformed preop- erative DTI images into data in Slicer to generate tracts for given points of interest (POI). } } @article{matsui2015prefrontal, title={Prefrontal cortex white matter tracts in prodromal Huntington disease}, author={Matsui, Joy T and Vaidya, Jatin G and Wassermann, Demian and Kim, Regina Eunyoung and Magnotta, Vincent A and Johnson, Hans J and Paulsen, Jane S}, journal={Human brain mapping}, volume={36}, number={10}, pages={3717--3732}, year={2015}, publisher={Wiley Online Library}, comment={Full brain tractography was performed on the unbiased DTI template using the streamline tractography module and recommended parameter settings available in 3D Slicer} } @article{nestor2015dissociating, title={Dissociating prefrontal circuitry in intelligence and memory: neuropsychological correlates of magnetic resonance and diffusion tensor imaging}, author={Nestor, Paul G and Ohtani, Toshiyuki and Bouix, Sylvain and Hosokawa, Taiga and Saito, Yukiko and Newell, Dominick T and Kubicki, Marek}, journal={Brain imaging and behavior}, volume={9}, number={4}, pages={839--847}, year={2015}, publisher={Springer}, comment={After the ROIs (ie bilateral ant mOFC, post mOFC, and rACC) were transferred to DTI space, stochastic tractography (part of Slicer3 software(www.slicer.org) was performed to generate white matter tract connections.} } @article{wolff2015altered, title={Altered corpus callosum morphology associated with autism over the first 2 years of life}, author={Wolff, Jason J. and Gerig, Guido and Lewis, John D. and Soda, Takahiro and Styner, Martin A. and Vachet, Clement and Botteron, Kelly N. and Elison, Jed T. and Dager, Stephen R. and Estes, Annette M. and Hazlett, Heather C. and Schultz, Robert T. and Zwaigenbaum, Lonnie and Piven, Joseph}, journal={Brain}, volume={138}, number={7}, pages={2046--2058}, year={2015}, publisher={Oxford Univ Press}, comment={Corpus callosum tractography was accomplished through seed label mapping of the midsagittal atlas image using 3D Slicer (www.slicer.org), } } @article{behdinan2015neuroimaging, title={Neuroimaging predictors of functional outcomes in schizophrenia at baseline and 6-month follow-up}, author={Behdinan, Tina and Foussias, George and Wheeler, Anne L and Stefanik, Laura and Felsky, Daniel and Remington, Gary and Rajji, Tarek K and Chakravarty, M Mallar and Voineskos, Aristotle N}, journal={Schizophrenia research}, volume={169}, number={1}, pages={69--75}, year={2015}, publisher={Elsevier}, comment={Tractography, creation of white matter fiber tracts, and clustering segmentation were performed using 3D Slicer (version 2) and Matlab (version 7.0)} } @article{mandl2015comparing, title={Comparing free water imaging and magnetization transfer measurements in schizophrenia}, author={Mandl, Rene CW and Pasternak, Ofer and Cahn, Wiepke and Kubicki, Marek and Kahn, Rene S and Shenton, Martha E and Pol, Hilleke E Hulshoff}, journal={Schizophrenia research}, volume={161}, number={1}, pages={126--132}, year={2015}, publisher={Elsevier}, comment={In the first step, all possible tracts in each brain were reconstructed individually in native DWI space using the single tensor fiber tracking algorithm implemented in the UKF Tractography library (Malcolm et al., 2010), which is part of the Slicer 3D software package } } @article{kruger2015three, title={Three distinct fiber pathways of the bed nucleus of the stria terminalis to the amygdala and prefrontal cortex}, author={Krüger, Oliver and Shiozawa, Thomas and Kreifelts, Benjamin and Scheffler, Klaus and Ethofer, Thomas}, journal={Cortex}, volume={66}, pages={60--68}, year={2015}, publisher={Elsevier}, comment={Fiber projections present in more than 75% of the participants were displayed using FSLView and 3D Slicer.} } @article{whitford2014localized, title={Localized abnormalities in the cingulum bundle in patients with schizophrenia: a diffusion tensor tractography study}, author={Whitford, Thomas J and Lee, Sun Woo and Oh, Jungsu S and de Luis-Garcia, Rodrigo and Savadjiev, Peter and Alvarado, Jorge L and Westin, Carl-Fredrik and Niznikiewicz, Margaret and Nestor, Paul G and McCarley, Robert W and Kubicki, M and Shenton, ME.}, journal={NeuroImage: Clinical}, volume={5}, pages={93--99}, year={2014}, publisher={Elsevier}, comment={Diffusion Tensor Images (DTIs) were estimated from the Diffusion-Weighted Images in Slicer v2.8 (http://www.slicer.org), on the basis of a weighted-least-squares estimation.} } @article{shaaban2014volumetric, title={Volumetric Assessment of Corticospinal Tract Infiltration by Astrocytoma Using Diffusion Tensor Tractography}, author={Shaaban, Marwa Adel and Alloush, Taha Kamel and Ibrahim, Mohamed Hamdy and Morad, Sherif Hashim}, journal={Open Journal of Medical Imaging}, volume={4}, number={2}, pages={65-71}, year={2014}, publisher={Scientific Research Publishing}, comment={First, fractional anisotropy maps were generated in each case, using the 3D-Slicer software. } } @article{verde2014unc, title={UNC-Utah NA-MIC framework for DTI fiber tract analysis}, author={Verde, Audrey and Budin, Francois and Berger, Jean-Baptiste and Gupta, Aditya and Farzinfar, Mahshid and Kaiser, Adrien and Ahn, Mihye and Johnson, Hans and Matsui, Joy and Hazlett, Heather and Sharma, Anuja and Goodlett, Casey and Shi, Yundi and Gouttard, Sylvain and Vachet, Clement and Piven, Joseph and Zhu, Hongtu and Gerig, Guido and Styner, Martin}, journal={Frontiers in neuroinformatics}, volume={7}, pages={51}, year={2014}, publisher={Frontiers}, comment={fiber tractography is performed via the label map tractography module or the full brain tractography module within 3D Slicer. } } @article{ho2014morphological, title={Morphological parameters associated with ruptured posterior communicating aneurysms}, author={Ho, Allen and Lin, Ning and Charoenvimolphan, Nareerat and Stanley, Mary and Frerichs, Kai U and Day, Arthur L and Du, Rose}, journal={PloS one}, volume={9}, number={4}, pages={1-7}, year={2014}, publisher={Public Library of Science}, comment={Measurements were performed manually taking advantage of the 3D slicer software fiducial tractography capabilities} } @article{penzkofer2014advanced, title={Advanced multimodal image-guided interventions and surgeries}, author={Penzkofer, Tobias and Jolesz, Ferenc A}, journal={Current Approaches in Image-Guided Therapy.}, volume={NA}, number={NA}, pages={21--34}, year={2014}, publisher={Future Medicine}, comment={3D Slicer showing a diffusion-tensor imaging tractography based on diffusion MRI} } @article{rojas2014stereoscopic, title={Stereoscopic three-dimensional visualization applied to multimodal brain images: clinical applications and a functional connectivity atlas}, author={Rojas, Gonzalo M and Galvez, Marcelo and Vega Potler, Natan and Craddock, R Cameron and Margulies, Daniel S and Castellanos, F Xavier and Milham, Michael P}, journal={Frontiers in neuroscience}, volume={8}, pages={328}, year={2014}, publisher={Frontiers}, comment={The tractography was processed using 3D Slicer 3.6.3 software.} } @article{ohtani2014abnormalities, title={Abnormalities in white matter connections between orbitofrontal cortex and anterior cingulate cortex and their associations with negative symptoms in schizophrenia: a DTI study}, author={Ohtani, Toshiyuki and Bouix, Sylvain and Hosokawa, Taiga and Saito, Yukiko and Eckbo, Ryan and Ballinger, Thomas and Rausch, Andrew and Melonakos, Eric and Kubicki, Marek}, journal={Schizophrenia research}, volume={157}, number={1}, pages={190--197}, year={2014}, publisher={Elsevier}, comment={Once ROIs were transferred to DTI space, stochastic tractography (http://www.slicer.org)) was performed to generate WM connections.} } @article{huttlova2014abnormalities, title={Abnormalities in myelination of the superior cerebellar peduncle in patients with schizophrenia and deficits in movement sequencing}, author={Huttlova, Jitka and Kikinis, Zora and Kerkovsky, Milos and Bouix, Sylvain and Vu, Mai-Anh and Makris, Nikos and Shenton, Martha and Kasparek, Tomas}, journal={The Cerebellum}, volume={13}, number={4}, pages={415--424}, year={2014}, publisher={Springer}, comment={ Tensor estimation and the following tractography were performed using the 3D Slicer software version 3.6.4-beta (http://?www.?slicer.?org/) } } @article{ohtani2014medial, title={Medial frontal white and gray matter contributions to general intelligence}, author={Ohtani, Toshiyuki and Nestor, Paul G and Bouix, Sylvain and Saito, Yukiko and Hosokawa, Taiga and Kubicki, Marek}, journal={PloS one}, volume={9}, number={12}, pages={1-17}, year={2014}, publisher={Public Library of Science}, comment={stochastic tractography (part of Slicer3 software (www.slicer.org)) was performed to generate WM connections.} } @article{avery2014bnst, title={BNST neurocircuitry in humans}, author={Avery, Suzanne N and Clauss, Jacqueline A and Winder, Danny G and Woodward, Neil and Heckers, Stephan and Blackford, Jennifer Urbano}, journal={Neuroimage}, volume={91}, pages={311--323}, year={2014}, publisher={Elsevier}, comment={The stria terminalis was traced in 3D Slicer (http://www.slicer.org)} } @article{oguz2014dtiprep, title={DTIPrep: quality control of diffusion-weighted images}, author={Oguz, Ipek and Farzinfar, Mahshid and Matsui, Joy and Budin, Francois and Liu, Zhexing and Gerig, Guido and Johnson, Hans J and Styner, Martin Andreas}, journal={Frontiers in neuroinformatics}, volume={8}, pages={4}, year={2014}, publisher={Frontiers}, comment={Finally, the reconstructed DTI image is assessed within 3D Slicer 3 , via a visualization of the local tensor orientations as well as investigative, interactive fiber tractography to assess anatomical fiber correctness. } } @article{fitzsimmons2014diffusion, title={Diffusion tensor imaging study of the fornix in first episode schizophrenia and in healthy controls}, author={Fitzsimmons, J and Hamoda, HM and Swisher, T and Terry, D and Rosenberger, G and Seidman, LJ and Goldstein, J and Mesholam-Gately, R and Petryshen, T and Wojcik, J and Kikinis, R. and Kubicki, M.}, journal={Schizophrenia research}, volume={156}, number={2}, pages={157--160}, year={2014}, publisher={Elsevier}, comment={Tensors were estimated using the Least Squares method (Tristan-Vega et al., 2009) and the 3DSlicer (www.slicer.org) software version 3.6.4} } @article{asami2014cerebral, title={Cerebral white matter abnormalities and their associations with negative but not positive symptoms of schizophrenia}, author={Asami, Takeshi and Lee, Sang Hyuk and Bouix, Sylvain and Rathi, Yogesh and Whitford, Thomas J and Niznikiewicz, Margaret and Nestor, Paul and McCarley, Robert W and Shenton, Martha E and Kubicki, Marek}, journal={Psychiatry Research: Neuroimaging}, volume={222}, number={1}, pages={52--59}, year={2014}, publisher={Elsevier}, comment={mean FAs of each region were calculated using 3D?Slicer.} } @article{hoogenboom2014cerebral, title={Cerebral white matter integrity and resting-state functional connectivity in middle-aged patients with type 2 diabetes}, author={Hoogenboom, Wouter S and Marder, Thomas J and Flores, Veronica L and Huisman, Susanne and Eaton, Hana P and Schneiderman, Jason S and Bolo, Nicolas R and Simonson, Donald C and Jacobson, Alan M and Kubicki, Marek and Shenton, Martha E. and Musen, Gail}, journal={Diabetes}, volume={63}, number={2}, pages={728--738}, year={2014}, publisher={Am Diabetes Assoc}, comment={All DTI analyses were performed with the 3DSlicer software package (http://slicer.org, Surgical Planning Laboratory, Brigham and Women's Hospital, Boston, MA). } } @article{fitzsimmons2014cingulum, title={Cingulum bundle diffusivity and delusions of reference in first episode and chronic schizophrenia}, author={Fitzsimmons, Jennifer and Schneiderman, Jason S and Whitford, Thomas J and Swisher, Tali and Niznikiewicz, Margaret A and Pelavin, Paula E and Terry, Douglas P and Mesholam-Gately, Raquelle I and Seidman, Larry J and Goldstein, Jill M and Kubicki, Marek}, journal={Psychiatry Research: Neuroimaging}, volume={224}, number={2}, pages={124--132}, year={2014}, publisher={Elsevier}, comment={we used the streamline tractography method that is one of the modules in the 3D Slicer software (http://www.slicer.org)} } @article{maraka2014degree, title={Degree of corticospinal tract damage correlates with motor function after stroke}, author={Maraka, Stefania and Jiang, Quan and Jafari-Khouzani, Kourosh and Li, Lian and Malik, Shaneela and Hamidian, Hajar and Zhang, Talan and Lu, Mei and Soltanian-Zadeh, Hamid and Chopp, Michael and Mitsias, Panayiotis D}, journal={Annals of clinical and translational neurology}, volume={1}, number={11}, pages={891--899}, year={2014}, publisher={Wiley Online Library}, comment={The MRI data were transferred to a computer workstation with Microsoft Windows operating system and were processed using 3D Slicer (version 3) open source image analysis software platform (www.slicer.com). The first step was to convert the diffusion weighted (DWI) DiCom images to nearly raw raster data (NRRD) format. Then, the DWI image was filtered in the mean squared error sense using a Rician noise model for noise reduction} } @article{peters2014brain, title={Brain white matter development is associated with a human-specific haplotype increasing the synthesis of long chain fatty acids}, author={Peters, Bart D. and Voineskos, Aristotle N. and Szeszko, Philip R. and Lett, Tristram A. and DeRosse, Pamela and Guha, Saurav and Karlsgodt, Katherine H. and Ikuta, Toshikazu and Felsky, Daniel and John, Majnu and Rotenberg, David J. and Kennedy, James L. and Lencz, Todd and Malhotra, Anil K.}, journal={The Journal of Neuroscience}, volume={34}, number={18}, pages={6367--6376}, year={2014}, publisher={Soc Neuroscience}, comment={Tractography and creation of white matter fiber tracts were performed using 3D Slicer (www.slicer.org) and MATLAB 7.0 (www.mathworks.com). } } @article{giordano2014connecting, title={Connecting fractional anisotropy from medical images with mechanical anisotropy of a hyperviscoelastic fibre-reinforced constitutive model for brain tissue}, author={Giordano, Chiara and Kleiven, Svein}, journal={Journal of The Royal Society Interface}, volume={11}, number={91}, pages={20130914}, year={2014}, publisher={The Royal Society}, comment={To determine the main direction, brain tractography is performed in 3D Slicer} } @article{egger2014white, title={White matter changes in patients with friedreich ataxia after treatment with erythropoietin}, author={Egger, Karl and Clemm von Hohenberg, Christian and Schocke, Michael F. and Guttmann, Charles R.G. and Wassermann, Demian and Wigand, Marlene C. and Nachbauer, Wolfgang and Kremser, Christian and Sturm, Brigitte and Scheiber-Mojdehkar, Barbara and Kubicki, Marek and Shenton, Martha E. and Boesch, Sylvia}, journal={Journal of Neuroimaging}, volume={24}, number={5}, pages={504--508}, year={2014}, publisher={Wiley Online Library}, comment={diffusion tensors were estimated using a weighted least squares method in Slicer (slicer.org)} } @article{juenger2014microstructure, title={Microstructure of transcallosal motor fibers reflects type of cortical (re-) organization in congenital hemiparesis}, author={Juenger, Hendrik and Koerte, Inga K and Muehlmann, Marc and Mayinger, Michael and Mall, Volker and Krageloh-Mann, Ingeborg and Shenton, Martha E and Berweck, Steffen and Staudt, Martin and Heinen, Florian}, journal={european journal of paediatric neurology}, volume={18}, number={6}, pages={691--697}, year={2014}, publisher={Elsevier}, comment={ Voxelwise diffusivity parameters including FA, RD , AD, and trace were calculated using 3D Slicer} } @article{cavallari2014thalamic, title={Thalamic fractional anisotropy predicts accrual of cerebral white matter damage in older subjects with small-vessel disease}, author={Cavallari, Michele and Moscufo, Nicola and Meier, Dominik and Skudlarski, Pawel and Pearlson, Godfrey D and White, William B and Wolfson, Leslie and Guttmann, Charles RG}, journal={Journal of Cerebral Blood Flow \& Metabolism}, volume={34}, number={8}, pages={1321--1327}, year={2014}, publisher={SAGE Publications}, comment={3D Slicer (www.slicer.org) was used for region of interest outlining, DTI metrics analysis, and WMH volume measurement.} } @article{giordano2014evaluation, title={Evaluation of axonal strain as a predictor for mild traumatic brain injuries using finite element modeling}, author={Giordano, Chiara and Kleiven, Svein}, journal={Stapp car crash journal}, volume={58}, pages={29}, year={2014}, publisher={The Stapp Association}, comment={The actual main direction of fiber in the brain (which may differ from the loading direction) is instead determined using brain tractography (3D SLICER). } } @article{hoogenboom2014limbic, title={Limbic system white matter microstructure and long-term treatment outcome in major depressive disorder: a diffusion tensor imaging study using legacy data}, author={Hoogenboom, Wouter S and Perlis, Roy H and Smoller, Jordan W and Zeng-Treitler, Qing and Gainer, Vivian S and Murphy, Shawn N and Churchill, Susanne E and Kohane, Isaac S and Shenton, Martha E and Iosifescu, Dan V}, journal={The World Journal of Biological Psychiatry}, volume={15}, number={2}, pages={122--134}, year={2014}, publisher={Taylor \& Francis}, comment={To quantify FA, we used the software package 3DSlicer (http://www.slicer.org), which provides tools such as diffusion tensor estimation, diffusion tensor scalar measurements, and it also allows for the viewing of ROIs in all three planes simultaneously} } @article{lemaire2013extended, title={Extended Broca's area in the functional connectome of language in adults: combined cortical and subcortical single-subject analysis using fMRI and DTI tractography}, author={Lemaire, Jean-Jacques and Golby, Alexandra and Wells III, William M and Pujol, Sonia and Tie, Yanmei and Rigolo, Laura and Yarmarkovich, Alexander and Pieper, Steve and Westin, Carl-Fredrik and Jolesz, Ferenc and Kikinis, Ron}, journal={Brain topography}, volume={26}, number={3}, pages={428--441}, year={2013}, publisher={Springer}, comment={DTI fiber tracking (streamline continuous diffusion tensor algorithm (P J Basser, Pajevic, Pierpaoli, Duda, & Aldroubi, 2000)) was performed in Slicer 3.3} } @article{voineskos2013neuroimaging, title={Neuroimaging evidence for the deficit subtype of schizophrenia}, author={Voineskos, Aristotle N and Foussias, George and Lerch, Jason and Felsky, Daniel and Remington, Gary and Rajji, Tarek K and Lobaugh, Nancy and Pollock, Bruce G and Mulsant, Benoit H}, journal={JAMA psychiatry}, volume={70}, number={5}, pages={472--480}, year={2013}, publisher={American Medical Association}, comment={Tractography, creation of white matter fiber tracts, and clustering segmentation were performed using the 3D Slicer (www.slicer.org) and Matlab, version 7.0 (The Mathworks Inc; http://www.mathworks.com).} } @article{makris2013human, title={Human middle longitudinal fascicle: segregation and behavioral-clinical implications of two distinct fiber connections linking temporal pole and superior temporal gyrus with the angular gyrus or superior parietal lobule using multi-tensor tractography}, author={Makris, N and Preti, MG and Wassermann, D and Rathi, Y and Papadimitriou, GM and Yergatian, C and Dickerson, BC and Shenton, ME and Kubicki, M}, journal={Brain imaging and behavior}, volume={7}, number={3}, pages={335--352}, year={2013}, publisher={Springer}, comment={diffusion tensors were estimated in 3D Slicer software (http://www.slicer.org), and then FA, AD and RD were calculated for each voxel; the 3D Slicer software package (http://www.slicer.org, https://github.com/pnlbwh/ukftractography), using a multi-tensor tractography algorithm.} } @inproceedings{verde2013unc, title={UNC-Utah NA-MIC DTI framework: atlas based fiber tract analysis with application to a study of nicotine smoking addiction}, author={Verde, Audrey R. and Berger, Jean-Baptiste and Gupta, Aditya and Farzinfar, Mahshid and Kaiser, Adrien and Chanon, Vicki W. and Boettiger, Charlotte and Johnson, Hans and Matsui, Joy and Sharma, Anuja and Goodlett, Casey and Shi, Yundi and Zhu, Hongtu and Gerig, Guido and Gouttard, Sylvain and Vachet, Clement and Styner, Martin}, booktitle={SPIE Medical Imaging}, pages={86692D--86692D}, year={2013}, organization={International Society for Optics and Photonics}, comment={fiber tractography is performed via the label map tractography module or the full brain tractography module within 3D Slicer.} } @article{inoue2013preliminary, title={Preliminary study on the clinical application of augmented reality neuronavigation}, author={Inoue, D and Cho, B and Mori, M and Kikkawa, Y and Amano, T and Nakamizo, A and Yoshimoto, K and Mizoguchi, M and Tomikawa, M and Hong, J and Hashizume, M. and Sasaki, T.}, journal={Journal of Neurological Surgery Part A: Central European Neurosurgery}, volume={74}, number={02}, pages={071--076}, year={2013}, publisher={Georg Thieme Verlag KG}, comment={We created diffusion tensor imaging (DTI) tractography using the labelmap seeding function of 3D Slicer. } } @article{de2013geometrical, title={Geometrical constraints for robust tractography selection}, author={de Luis-Garcia, Rodrigo and Westin, Carl-Fredrik and Alberola-Lopez, Carlos}, journal={Neuroimage}, volume={81}, pages={26--48}, year={2013}, publisher={Elsevier}, comment={With regard to tractography, whole-brain deterministic tractography was performed using Slicer 3.6 (http://www.slicer.org), using an FA mask thresholded at 0.2.} } @article{makris2013human2, title={Human middle longitudinal fascicle: variations in patterns of anatomical connections}, author={Makris, N and Preti, MG and Asami, T and Pelavin, P and Campbell, B and Papadimitriou, GM and Kaiser, J and Baselli, G and Westin, Carl-Fredrik and Shenton, ME and Kubicki, M.}, journal={Brain Structure and Function}, volume={218}, number={4}, pages={951--968}, year={2013}, publisher={Springer}, comment={Diffusion tractography was performed in 3D-slicer (v2.7, www.?slicer.?org).} } @article{kubicki2013decreased, title={Decreased axial diffusivity within language connections: a possible biomarker of schizophrenia risk}, author={Kubicki, M and Shenton, ME and Maciejewski, PK and Pelavin, PE and Hawley, KJ and Ballinger, T and Swisher, T and Jabbar, GA and Thermenos, HW and Keshavan, MS and Seidman, LJ and Delisi, LE.}, journal={Schizophrenia research}, volume={148}, number={1}, pages={67--73}, year={2013}, publisher={Elsevier}, comment={For delineation of UF, AF, and IOFF, we used a streamline tractography method, using Slicer 3D software. } } @article{asami2013abnormalities, title={Abnormalities of middle longitudinal fascicle and disorganization in patients with schizophrenia}, author={Asami, Takeshi and Saito, Yukiko and Whitford, Thomas J and Makris, Nikos and Niznikiewicz, Margaret and McCarley, Robert W and Shenton, Martha E and Kubicki, Marek}, journal={Schizophrenia research}, volume={143}, number={2}, pages={253--259}, year={2013}, publisher={Elsevier}, comment={Measurements of the MdLF were performed using 3D-slicer (v2.7, gro.recils.www) and diffusion tensor tractography. } } @article{farzinfar2013diffusion, title={Diffusion imaging quality control via entropy of principal direction distribution}, author={Farzinfar, Mahshid and Oguz, Ipek and Smith, Rachel G and Verde, Audrey R and Dietrich, Cheryl and Gupta, Aditya and Escolar, Maria L and Piven, Joseph and Pujol, Sonia and Vachet, Clement and Gouttard, Sylvain and Gerig, Guido and Dager, Stephen and McKinstry, Robert C. and Paterson, Sarah and Evans, Alan C. and Styner, Martin A.}, journal={Neuroimage}, volume={82}, pages={1--12}, year={2013}, publisher={Elsevier}, comment={3D Slicer tool is used for tractography using fiducial seeds} } @article{grigis2013longitudinal, title={Longitudinal change detection: Inference on the diffusion tensor along white matter pathways}, author={Grigis, Antoine and Noblet, Vincent and Blanc, Frederic and Heitz, Fabrice and de Seze, Jerome and Kremer, Stephane and Armspach, Jean-Paul}, journal={Medical image analysis}, volume={17}, number={3}, pages={375--386}, year={2013}, publisher={Elsevier}, comment={Then, a fiber tract extraction is performed with Slicer 2 on each of the two exams} } @article{li2013decompressive, title={Decompressive craniectomy causes a significant strain increase in axonal fiber tracts}, author={Li, Xiaogai and von Holst, Hans and Kleiven, Svein}, journal={Journal of clinical neuroscience}, volume={20}, number={4}, pages={509--513}, year={2013}, publisher={Elsevier}, comment={diffusion tensors were then estimated using a standard least-squares method implemented in the Slicer 3D software,} } @inproceedings{stender2013detecting, title={Detecting rat heart myocardial fiber directions in x-ray microtomography using coherence-enhancing diffusion filtering}, author={Stender, Birgit and Schlaefer, Alexander}, booktitle={International Conference on Functional Imaging and Modeling of the Heart}, pages={63--70}, year={2013}, organization={Springer}, comment={We used 3D Slicer for fiber tracking} } @article{kikinis2013genetic, title={Genetic contributions to changes of fiber tracts of ventral visual stream in 22q11. 2 deletion syndrome}, author={Kikinis, Zora and Makris, Nikos and Finn, Christine T and Bouix, Sylvain and Lucia, Diandra and Coleman, Michael J and Tworog-Dube, Erica and Kikinis, Ron and Kucherlapati, Raju and Shenton, Martha E and Kubicki, M.}, journal={Brain imaging and behavior}, volume={7}, number={3}, pages={316--325}, year={2013}, publisher={Springer}, comment={Tensors were estimated using least squares method (Basser \& Jones, 2002) implemented in 3DSlicer software version 2.8. (http://www.slicer.org/).} } @article{short2013associations, title={Associations between white matter microstructure and infants' working memory}, author={Short, Sarah J and Elison, Jed T and Goldman, Barbara Davis and Styner, Martin and Gu, Hongbin and Connelly, Mark and Maltbie, Eric and Woolson, Sandra and Lin, Weili and Gerig, Guido and Reznick JS and Gilmore JH.}, journal={Neuroimage}, volume={64}, pages={156--166}, year={2013}, publisher={Elsevier}, comment={Standard streamline DTI tractography (Fillard and Gerig, 2003) was performed on a pediatric atlas built from all 1-year old study subjects (see Fig. 1) using 3D Slicer (version 3.6.3) (http://www.slicer.org). } } @article{martin2013mr, title={MR-DTI RICIAN DENOISING}, author={Martin, Adrian and Garamendi, Juan F and Schiavi, Emanuele}, journal={Dyna}, volume={80}, number={182}, pages={25--30}, year={2013}, publisher={2006, Revista DYNA}, comment={the Diffusion Tensorial Image reconstruction, which was done with the 3d Slicer tools (freely available at http://www.slicer.org).} } @article{irimia2013structural, title={The structural, connectomic and network covariance of the human brain}, author={Irimia, Andrei and Van Horn, John D}, journal={Neuroimage}, volume={66}, pages={489--499}, year={2013}, publisher={Elsevier}, comment={The 3D Slicer (http://slicer.org) program, an openly available software platform from the National Alliance for Medical Image Computing (NA-MIC; http://www.na-mic.org) for visualization. } } @article{elison2013frontolimbic, title={Frontolimbic neural circuitry at 6 months predicts individual differences in joint attention at 9 months}, author={Elison, Jed T and Wolff, Jason J and Heimer, Debra C and Paterson, Sarah J and Gu, Hongbin and Hazlett, Heather C and Styner, Martin and Gerig, Guido and Piven, Joseph}, journal={Developmental science}, volume={16}, number={2}, pages={186--197}, year={2013}, publisher={Wiley Online Library}, comment={Seed label maps for the inferior longitudinal fasciculus (ILF), uncinate fasciculus (UF), and optic nerve were created based on methods described in existing white matter tractography atlases (Catani \& Thiebaut de Schotten, 2008; Mori, Wakana, Nagae-Poetscher, \& van Zilj, 2005) using 3D Slicer (www.slicer.org). } } @article{voineskos2013oligodendrocyte, title={Oligodendrocyte genes, white matter tract integrity, and cognition in schizophrenia}, author={Voineskos, Aristotle N. and Felsky, Daniel and Kovacevic, Natasa and Tiwari, Arun K. and Zai, Clement and Chakravarty, M. Mallar and Lobaugh, Nancy J. and Shenton, Martha E. and Rajji, Tarek K. and Miranda, Dielle and Pollock, Bruce G. and Mulsant, Benoit H. and McIntosh, Anthony R. and Kennedy, James L.}, journal={Cerebral cortex}, volume={23}, number={9}, pages={2044--2057}, year={2013}, publisher={Oxford Univ Press}, comment={Tractography and creation of white matter fiber tracts were performed using 3D Slicer (www.slicer.org) and Matlab 7.0 (www.mathworks.com).} } @article{buijink2013decreased, title={Decreased cerebellar fiber density in cortical myoclonic tremor but not in essential tremor}, author={Buijink, Arthur WG and Caan, Matthan WA and Tijssen, Marina AJ and Hoogduin, Johannes M and Maurits, Natasha M and van Rootselaar, Anne-Fleur}, journal={The Cerebellum}, volume={12}, number={2}, pages={199--204}, year={2013}, publisher={Springer}, comment={AFvR annotated the cerebellum based on FA- and mean diffusivity volumes using 3D-Slicer (http://?www.?slicer.?org). } } @article{schulte2013fiber, title={Fiber tract-driven topographical mapping (FTTM) reveals microstructural relevance for interhemispheric visuomotor function in the aging brain}, author={Schulte, Tilman and Maddah, Mahnaz and Muller-Oehring, Eva M and Rohlfing, Torsten and Pfefferbaum, Adolf and Sullivan, Edith V}, journal={Neuroimage}, volume={77}, pages={195--206}, year={2013}, publisher={Elsevier}, comment={streamline tractography for each subject, seeded from the mapped labeled atlas regions, was performed in native subject DTI image space using 3D Slicer3 (http://www.slicer.org) (Fedorov et al., 2012). } } @article{elison2013white, title={White matter microstructure and atypical visual orienting in 7-month-olds at risk for autism}, author={Elison, Jed T and Paterson, Sarah J and Wolff, Jason J and Reznick, J Steven and Sasson, Noah J and Gu, Hongbin and Botteron, Kelly N and Dager, Stephen R and Estes, Annette M and Evans, Alan C and Gerig, G and Hazlett, HC and Schultz, RT and Styner, M and Zwaigenbaum, L and Piven J and IBIS Network}, journal={American Journal of Psychiatry}, volume={170}, number={8}, pages={899-908}, year={2013}, publisher={Am Psychiatric Assoc}, comment={Deterministic tractography was performed by manually drawing seed label maps for the splenium and genu of the corpus callosum and the left and right corticospinal tracts (broadly defined as corticospinal pathways passing through the posterior limb of the internal capsule) based on methods described previously (29) using the 3DSlicer program (www.slicer.org) (Figure 2).} } @article{wu2012visual, title={Visual pathway study using in vivo DTI tractography to complement classical anatomy}, author={Wu, Wentao and Rigolo, Laura and O'Donnell, Lauren J and Norton, Isaiah and Shriver, Sargent and Golby, Alexandra J}, journal={Neurosurgery}, volume={70}, number={OPERATIVE}, pages={ons145}, year={2012}, publisher={NIH Public Access}, comment={Using a fiducial-based DTI tractography tool (Slicer 3.3), seeds were placed near the lateral geniculate nucleus (LGN) to reconstruct individual visual pathways and neighboring tracts.} } @article{hodaie2012tractography, title={Tractography delineates microstructural changes in the trigeminal nerve after focal radiosurgery for trigeminal neuralgia}, author={Hodaie, Mojgan and Chen, David Qixiang and Quan, Jessica and Laperriere, Normand}, journal={PloS one}, volume={7}, number={3}, pages={e32745}, year={2012}, publisher={Public Library of Science}, comment={ Images were processed, registered and tractography were performed using the 3D Slicer software} } @article{rosenberger2012anterior, title={Anterior limb of the internal capsule in schizophrenia: a diffusion tensor tractography study}, author={Rosenberger, Gudrun and Nestor, Paul G and Oh, Jungsu S and Levitt, James J and Kindleman, Gordon and Bouix, Sylvain and Fitzsimmons, Jennifer and Niznikiewicz, Margaret and Westin, Carl-Fredrik and Kikinis, Ron and McCarley, RW and Shenton, ME and Kubicki, M.}, journal={Brain imaging and behavior}, volume={6}, number={3}, pages={417--425}, year={2012}, publisher={Springer}, comment={3D Slicer (www.?slicer.?org) was used for diffusion tensor tractography based on whole-white matter seeding. } } @article{voineskos2012age, title={Age-related decline in white matter tract integrity and cognitive performance: a DTI tractography and structural equation modeling study}, author={Voineskos, Aristotle N and Rajji, Tarek K and Lobaugh, Nancy J and Miranda, Dielle and Shenton, Martha E and Kennedy, James L and Pollock, Bruce G and Mulsant, Benoit H}, journal={Neurobiology of aging}, volume={33}, number={1}, pages={21--34}, year={2012}, publisher={Elsevier}, comment={Tractography and creation of white matter fiber tracts was performed using 3D Slicer (open source software; www.slicer.org) and MATLAB 7.0 (www.mathworks.com).} } @article{oh2012reduced, title={Reduced fronto-callosal fiber integrity in unmedicated OCD patients: A diffusion tractography study}, author={Oh, Jungsu S and Jang, Joon Hwan and Jung, Wi Hoon and Kang, Do-Hyung and Choi, Jung-Seok and Choi, Chi-Hoon and Kubicki, Marek and Shenton, Martha E and Kwon, Jun Soo}, journal={Human brain mapping}, volume={33}, number={10}, pages={2441--2452}, year={2012}, publisher={Wiley Online Library}, comment={a small percentage of unwanted tracts produced by DTI noises, were regular- ized using the sensitivity tool developed by Estepar et al. [2006] (part of Slicer package?www.slicer.org) and applied to a schizophrenia study [Fitzsimmons et al., 2009]. (not sure)} } @inproceedings{farzinfar2012entropy, title={Entropy based DTI quality control via regional orientation distribution}, author={Farzinfar, Mahshid and Dietrich, Cheryl and Smith, Rachel Gimpel and Li, Yinpeng and Gupta, Aditya and Liu, Zhexing and Styner, Martin Andreas}, booktitle={IEEE International Symposium on Biomedical Imaging (ISBI)}, pages={22--25}, year={2012}, organization={IEEE}, comment={For both datasets, a set of artifact-free scans were first detected via visual assessment of the colorized FA, as well as manually guided streamline fiber tractography within 3D Slicer (by rater CD)} } @article{mulert2012hearing, title={Hearing voices: a role of interhemispheric auditory connectivity?}, author={Mulert, Christoph and Kirsch, Valerie and Whitford, Thomas J and Alvarado, Jorge and Pelavin, Paula and McCarley, Robert W and Kubicki, Marek and Salisbury, Dean F and Shenton, Martha E}, journal={The World Journal of Biological Psychiatry}, volume={13}, number={2}, pages={153--158}, year={2012}, publisher={Taylor \& Francis}, comment={Deterministic (streamline) tractography was implemented in the Slicer 2.7. software package (www.slicer.org), as described previously} } @article{koob2012thick, title={Thick corpus callosum: a clue to the diagnosis of fetal septopreoptic holoprosencephaly?}, author={Koob, Meriam and Weingertner, Anne-sophie and Gasser, Bernard and Oubel, Estanislao and Dietemann, Jean-Louis}, journal={Pediatric radiology}, volume={42}, number={7}, pages={886--890}, year={2012}, publisher={Springer}, comment={Tractography of the CC was performed using the standard streamline method implemented in Slicer (http://?slicer.?org)} } @inproceedings{liu2012unsupervised, title={Unsupervised automatic white matter fiber clustering using a Gaussian mixture model}, author={Liu, Meizhu and Vemuri, Baba C and Deriche, Rachid}, booktitle={IEEE International Symposium on Biomedical Imaging (ISBI)}, pages={522--525}, year={2012}, organization={IEEE}, comment={The tractography was performed using Slicer, and the stream-line tractography was implemented by seeding in sub-voxel resolution by taking every voxel with fractional anisotropy higher than 0.1} } @inproceedings{peronivmat, title={VMAT inverse planning including DTI tractography fiber bundles as organs at risk: a feasibility study}, author={Peroni, M and Patete, P and Ghielmetti, F and Casolino, D and Ongania, E and Casolino, DS and Fariselli, L and Baroni, G}, booktitle={Image-Guidance and Multimodal Dose Planning in Radiation Therapy}, pages={34}, year={2012}, comment={The corpus callosus, the corticospinal tract and the arcuate fasciculus ipsilateral to the neoplastic lesion were reconstructed using Slicer3D } } @inproceedings{oguz2012minimum, title={A minimum cost approach to connectivity from orientation distribution functions via efficient multi-directional graph propagation}, author={Oguz, Ipek and Boucharin, Alexis and Lu, Wenyu and Vachet, Clement and Budin, Francois and Shi, Yundi and Styner, Martin}, booktitle={Proceedings of CDMRI Workshop, MICCAI 2012}, pages={210--221}, year={2012}, comment={We have also computed streamline tractography (using Slicer3, www.slicer.org) for illustrating the 'true' paths.} } @article{baugh2012chronic, title={Chronic traumatic encephalopathy: neurodegeneration following repetitive concussive and subconcussive brain trauma}, author={Baugh, Christine M and Stamm, Julie M and Riley, David O and Gavett, Brandon E and Shenton, Martha E and Lin, Alexander and Nowinski, Christopher J and Cantu, Robert C and McKee, Ann C and Stern, Robert A}, journal={Brain imaging and behavior}, volume={6}, number={2}, pages={244--254}, year={2012}, publisher={Springer}, comment={Diffusion tensor images captured on a 3T magnet analyzed with streamline tractography using Slicer 3.} } @article{oubel2012reconstruction, title={Reconstruction of scattered data in fetal diffusion MRI}, author={Oubel, Estanislao and Koob, Meriam and Studholme, Colin and Dietemann, Jean-Louis and Rousseau, Francois}, journal={Medical image analysis}, volume={16}, number={1}, pages={28--37}, year={2012}, publisher={Elsevier}, comment={Tensors were estimated by using a standard least squares method, and the tractography was performed by applying a streamline method. In both cases we have used the algorithms implemented in Slicer.} } @article{choi2011diffusion, title={Diffusion tensor imaging of anterior commissural fibers in patients with schizophrenia}, author={Choi, Hongyoon and Kubicki, Marek and Whitford, Thomas J and Alvarado, Jorge L and Terry, Douglas P and Niznikiewicz, Margaret and McCarley, Robert W and Kwon, Jun Soo and Shenton, Martha E}, journal={Schizophrenia research}, volume={130}, number={1}, pages={78--85}, year={2011}, publisher={Elsevier}, comment={We utilized Slicer 3D software Version 2 (www.slicer.org) to analyze the images and to measure tracts.} } @inproceedings{wassermann2011white, title={White matter bundle registration and population analysis based on Gaussian processes}, author={Wassermann, Demian and Rathi, Yogesh and Bouix, Sylvain and Kubicki, Marek and Kikinis, Ron and Shenton, Martha and Westin, Carl-Fredrik}, booktitle={Biennial International Conference on Information Processing in Medical Imaging}, pages={320--332}, year={2011}, organization={Springer}, comment={The left uncinate and fronto-occipital fasciculi ROI's were manually drawn by experts using 3D Slicer (www.slicer.org) and fiber tracts were obtained using two-tensor tractography [17].} } @article{kikinis2012reduced, title={Reduced fractional anisotropy and axial diffusivity in white matter in 22q11. 2 deletion syndrome: a pilot study}, author={Kikinis, Z and Asami, T and Bouix, S and Finn, CT and Ballinger, T and Tworog-Dube, E and Kucherlapati, R and Kikinis, R and Shenton, ME and Kubicki, M}, journal={Schizophrenia research}, volume={141}, number={1}, pages={35--39}, year={2012}, publisher={Elsevier}, comment={ FA, AD and RD were calculated using 3DSlicer software (http://www.slicer.org/)} } @article{shi2012diffusion, title={Diffusion tensor imaging-based characterization of brain neurodevelopment in primates}, author={Shi, Yundi and Short, Sarah J and Knickmeyer, Rebecca C and Wang, Jiaping and Coe, Christopher L and Niethammer, Marc and Gilmore, John H and Zhu, Hongtu and Styner, Martin A}, journal={Cerebral Cortex}, volume={23}, number={1}, pages={36-48}, year={2012}, publisher={Oxford Univ Press}, comment={In our work, we performed ?ber tracking in the DTI atlas space with Slicer3 (http://www.slicer.org} } @article{whitford2011electrophysiological, title={Electrophysiological and diffusion tensor imaging evidence of delayed corollary discharges in patients with schizophrenia}, author={Whitford, TJ and Mathalon, DH and Shenton, ME and Roach, BJ and Bammer, R and Adcock, RA and Bouix, S and Kubicki, M and De Siebenthal, J and Rausch, AC and Schneiderman, JS and Ford, JM}, journal={Psychological medicine}, volume={41}, number={5}, pages={959}, year={2011}, publisher={Cambridge Univ Press}, comment={The left arcuate fasciculus was extracted from the DT images using deterministic tractography (Rosenberger et al. 2008), implemented in the Slicer-3 software package (www.slicer.org).} } @article{voineskos2011brain, title={The brain-derived neurotrophic factor Val66Met polymorphism and prediction of neural risk for Alzheimer disease}, author={Voineskos, Aristotle N and Lerch, Jason P and Felsky, Daniel and Shaikh, Sajid and Rajji, Tarek K and Miranda, Dielle and Lobaugh, Nancy J and Mulsant, Benoit H and Pollock, Bruce G and Kennedy, James L}, journal={Archives of General Psychiatry}, volume={68}, number={2}, pages={198--206}, year={2011}, publisher={American Medical Association}, comment={Tractography and creation of white matter fiber tracts were performed using the 3D Slicer (www.slicer.org) and MATLAB 7.0 (The Mathworks Inc, Natwick, Massachusetts; www.mathworks.com).} } @inproceedings{maddah2011sheet, title={Sheet-like white matter fiber tracts: representation, clustering, and quantitative analysis}, author={Maddah, Mahnaz and Miller, James V and Sullivan, Edith V and Pfefferbaum, Adolf and Rohlfing, Torsten}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={191--199}, year={2011}, organization={Springer}, comment={Streamline tractography was performed using 3D Slicer, seeded from the mapped labeled regions of CC and rCST (Fig. 4a), and terminated when an FA value less than 0.15, or maximum curvature of 0.8 was reached.} } @inproceedings{forsberg2011improving, title={Improving registration using multi-channel diffeomorphic demons combined with certainty maps}, author={Forsberg, Daniel and Rathi, Yogesh and Bouix, Sylvain and Wassermann, Demian and Knutsson, Hans and Westin, Carl-Fredrik}, booktitle={International Workshop on Multimodal Brain Image Analysis}, pages={19--26}, year={2011}, organization={Springer}, comment={The tractography was done using the Slicer software, where corpus callosum of each subject was handsegmented and then used as seeding points for standard single-tensor tractography.} } @inproceedings{grigis2011longitudinal, title={Longitudinal change detection: inference on the diffusion tensor along white-matter pathways}, author={Grigis, Antoine and Noblet, Vincent and Blanc, Frederic and Heitz, Fabrice and de Seze, Jerome and Armspach, Jean-Paul}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={1--8}, year={2011}, organization={Springer}, comment={the result of the clustering step on a tractography obtained with Slicer from a ROI in the corpus callosum (parameters: see text)} } @article{elhawary2011intra, title={Intra-operative real-time querying of white matter tracts during frameless stereotactic neuronavigation}, author={Elhawary, Haytham and Liu, Haiying and Patel, Pratik and Norton, Isaiah and Rigolo, Laura and Papademetris, Xenophon and Hata, Nobuhiko and Golby, Alexandra J}, journal={Neurosurgery}, volume={68}, number={2}, pages={506}, year={2011}, publisher={NIH Public Access}, comment={Tractography for the entire brain was performed using the 2 nd order Runge-Kutta method implemented in 3D Slicer.} } @article{kubicki2011stochastic, title={Stochastic tractography study of inferior frontal gyrus anatomical connectivity in schizophrenia}, author={Kubicki, Marek and Alvarado, Jorge L and Westin, Carl-Fredrik and Tate, David F and Markant, Douglas and Terry, Douglas P and Whitford, Thomas J and De Siebenthal, Julien and Bouix, Sylvain and McCarley, Robert W and Kikinis, R. and Shenton, ME}, journal={Neuroimage}, volume={55}, number={4}, pages={1657--1664}, year={2011}, publisher={Elsevier}, comment={Once ROIs were transferred into the DTI space, stochastic tractography was performed (using freely available module, part of 3D Slicer software) to generate white matter connections.} } @article{chen2011three, title={Three-dimensional in vivo modeling of vestibular schwannomas and surrounding cranial nerves with diffusion imaging tractography}, author={Chen, David Qixiang and Quan, Jessica and Guha, Abhijit and Tymianski, Michael and Mikulis, David and Hodaie, Mojgan}, journal={Neurosurgery}, volume={68}, number={4}, pages={1077--1083}, year={2011}, publisher={LWW}, comment={Both anatomic and DTI images were imported into 3D Slicer for tractography generation and 3D tumor modeling.} } @article{golby2011interactive, title={Interactive diffusion tensor tractography visualization for neurosurgical planning}, author={Golby, Alexandra J and Kindlmann, Gordon and Norton, Isaiah and Yarmarkovich, Alexander and Pieper, Steven and Kikinis, Ron}, journal={Neurosurgery}, volume={68}, number={2}, pages={496}, year={2011}, publisher={NIH Public Access}, comment={As implemented in 3D Slicer, the white matter tract trajectories are estimated using a single tensor model.} } @article{voineskos2011znf804a, title={The ZNF804A gene: characterization of a novel neural risk mechanism for the major psychoses}, author={Voineskos, Aristotle N and Lerch, Jason P and Felsky, Daniel and Tiwari, Arun and Rajji, Tarek K and Miranda, Dielle and Lobaugh, Nancy J and Pollock, Bruce G and Mulsant, Benoit H and Kennedy, James L}, journal={Neuropsychopharmacology}, volume={36}, number={9}, pages={1871--1878}, year={2011}, publisher={Nature Publishing Group}, comment={Tractography and creation of white matter fiber tracts were performed using 3D Slicer (http://www.slicer.org) and Matlab 7.0 (http://www.mathworks.com).} } @article{whitford2011fiber, title={Fiber geometry in the corpus callosum in schizophrenia: evidence for transcallosal misconnection}, author={Whitford, Thomas J and Savadjiev, Peter and Kubicki, Marek and O'Donnell, Lauren J and Terry, Douglas P and Bouix, Sylvain and Westin, Carl-Fredrik and Schneiderman, Jason S and Bobrow, Laurel and Rausch, Andrew C and Niznikiewicz, M and Nestor, PG and Pantelis, C and Wood, SJ and McCarley, RW and Shenton, ME.}, journal={Schizophrenia research}, volume={132}, number={1}, pages={69--74}, year={2011}, publisher={Elsevier} } @article{koerte2011anisotropy, title={Anisotropy of transcallosal motor fibres indicates functional impairment in children with periventricular leukomalacia}, author={KOERTE, INGA and PELAVIN, PAULA and KIRMESS, BERIT and FUCHS, TERESA and BERWECK, STEFFEN and LAUBENDER, RUEDIGER P and BORGGRAEFE, INGO and SCHROEDER, SEBASTIAN and DANEK, ADRIAN and RUMMENY, CLAUDIA and REISER, MAXIMILIAN and KUBICKI, MAREK and SHENTON, MARTHA E and ERTL-WAGNER, BIRGIT and HEINEN, FLORIAN}, journal={Developmental Medicine \& Child Neurology}, volume={53}, number={2}, pages={179--186}, year={2011}, publisher={Wiley Online Library}, comment={Tractography of the CST was performed in 3DSlicer by placing a ROI in the M1 and another in the ipsilateral, anterior part of the pons.} } @article{gerig2011synergy, title={Synergy of image analysis for animal and human neuroimaging supports translational research on drug abuse}, author={Gerig, Guido and Oguz, Ipek and Gouttard, Sylvain and Lee, Joohwi and An, Hongyu and Lin, Weili and McMurray, Matthew and Grewen, Karen and Johns, Josephine and Styner, Martin Andreas}, journal={Frontiers in psychiatry}, volume={2}, pages={53}, year={2011}, publisher={Frontiers}, comment={DTI fibers on the DTI altas are computed with standard streamline tractography in 3D Slicer.} } @article{wang2011dti, title={DTI registration in atlas based fiber analysis of infantile Krabbe disease}, author={Wang, Yi and Gupta, Aditya and Liu, Zhexing and Zhang, Hui and Escolar, Maria L and Gilmore, John H and Gouttard, Sylvain and Fillard, Pierre and Maltbie, Eric and Gerig, Guido and Styner, M.}, journal={Neuroimage}, volume={55}, number={4}, pages={1577--1586}, year={2011}, publisher={Elsevier}, comment={ Fig. 2(d) shows the 3D color visualization of the target fiber tracts genu (red), splenium (yellow), right hemisphere internal capsule (purple), left hemisphere internal capsule (blue) and uncinate (green) with Slicer} } @article{whitford2011predicting, title={Predicting inter-hemispheric transfer time from the diffusion properties of the corpus callosum in healthy individuals and schizophrenia patients: a combined ERP and DTI study}, author={Whitford, Thomas J and Kubicki, Marek and Ghorashi, Shahab and Schneiderman, Jason S and Hawley, Kathryn J and McCarley, Robert W and Shenton, Martha E and Spencer, Kevin M}, journal={Neuroimage}, volume={54}, number={3}, pages={2318--2329}, year={2011}, publisher={Elsevier}, comment={All DTI analysis was performed with the 3D-Slicer software package} } @article{jakab2011glioma, title={Glioma grade assessment by using histogram analysis of diffusion tensor imaging-derived maps}, author={Jakab, Andras and Molnar, Peter and Emri, Miklos and Berenyi, Ervin}, journal={Neuroradiology}, volume={53}, number={7}, pages={483--491}, year={2011}, publisher={Springer}, comment={The diffusion-weighted image conversion, diffusion metric calculations, and visualizations were carried out using the 3D Slicer 2.8 software } } @phdthesis{voineskos2010imaging, title={Imaging and Genetics Investigations in Schizophrenia and Aging: A Focus on White Matter}, author={Voineskos, Aristotle Nicholas}, year={2010}, school={University of Toronto}, comment={Tractography and creation of white matter fiber tracts were performed using 3D Slicer and Matlab 7.0.} } @article{zhu2010frats, title={FRATS: Functional regression analysis of dti tract statistics}, author={Zhu, Hongtu and Styner, Martin and Tang, Niansheng and Liu, Zhexing and Lin, Weili and Gilmore, John H}, journal={IEEE transactions on medical imaging}, volume={29}, number={4}, pages={1039--1049}, year={2010}, publisher={IEEE}, comment={Major fiber bundles are tracked in the atlas space within 3D Slicer.} } @article{levitt2010diffusion, title={A diffusion tensor imaging study of the anterior limb of the internal capsule in schizophrenia}, author={Levitt, James J and Kubicki, Marek and Nestor, Paul G and Ersner-Hershfield, Hal and Westin, Carl-Fredrik and Alvarado, Jorge L and Kikinis, Ron and Jolesz, Ferenc A and McCarley, Robert W and Shenton, Martha E}, journal={Psychiatry Research: Neuroimaging}, volume={184}, number={3}, pages={143--150}, year={2010}, publisher={Elsevier}, comment={To quantify internal capsule FA, we used the 3D-Slicer (http://www.slicer.org) which provides tools for the manual tracing of Region of Interests (ROIs) including allowing the viewing of ROIs in all 3 planes simultaneously.} } @article{whitford2010corpus, title={Corpus callosum abnormalities and their association with psychotic symptoms in patients with schizophrenia}, author={Whitford, Thomas J and Kubicki, Marek and Schneiderman, Jason S and O'Donnell, Lauren J and King, Rebecca and Alvarado, Jorge L and Khan, Usman and Markant, Douglas and Nestor, Paul G and Niznikiewicz, Margaret and McCarley, Robert W. and Westin, Carl-Fredrik and Shentona, Martha E.}, journal={Biological psychiatry}, volume={68}, number={1}, pages={70--77}, year={2010}, publisher={Elsevier}, comment={Tractography and fiber clustering were performed using Matlab 7.0 (www.mathworks.com) and 3D-Slicer.} } @article{voineskos2010role, title={The role of the corpus callosum in transcranial magnetic stimulation induced interhemispheric signal propagation}, author={Voineskos, Aristotle N and Farzan, Faranak and Barr, Mera S and Lobaugh, Nancy J and Mulsant, Benoit H and Chen, Robert and Fitzgerald, Paul B and Daskalakis, Zafiris J}, journal={Biological psychiatry}, volume={68}, number={9}, pages={825--831}, year={2010}, publisher={Elsevier}, comment={Tractography and creation of white-matter fiber tracts were performed using 3D Slicer (open source software, http://www.slicer.org) and MATLAB.} } @inproceedings{oubel2010reconstruction, title={Reconstruction of scattered data in fetal diffusion MRI}, author={Oubel, Estanislao and Koob, Meriam and Studholme, Colin and Dietemann, Jean-Louis and Rousseau, Francois}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={574--581}, year={2010}, organization={Springer}, comment={Tensors were estimated by using a standard least squares method, and the tractography was performed by applying a streamline method. In both cases we have used the algorithms implemented in Slicer.} } @article{savadjiev2010local, title={Local white matter geometry from diffusion tensor gradients}, author={Savadjiev, Peter and Kindlmann, Gordon L and Bouix, Sylvain and Shenton, Martha E and Westin, Carl-Fredrik}, journal={NeuroImage}, volume={49}, number={4}, pages={3175--3186}, year={2010}, publisher={Elsevier}, comment={After computation of the indices, standard streamline tractography [18] (Slicer reference) was run to help visualize in three dimensions the behaviour of the indices relative to well-known fibres.} } @inproceedings{gao2010fast, title={Fast Hamilton-Jacobi equation solver and neural fiber bundle extraction}, author={Gao, Yi and Melonakos, John and Tannenbaum, Allen}, booktitle={SPIE Medical Imaging}, pages={76231F--76231F}, year={2010}, organization={International Society for Optics and Photonics}, comment={The pipeline is integrated into the publicly available software 3D Slicer.} } @article{propper2010combined, title={A combined fMRI and DTI examination of functional language lateralization and arcuate fasciculus structure: Effects of degree versus direction of hand preference}, author={Propper, Ruth E and O'Donnell, Lauren J and Whalen, Stephen and Tie, Yanmei and Norton, Isaiah H and Suarez, Ralph O and Zollei, Lilla and Radmanesh, Alireza and Golby, Alexandra J}, journal={Brain and cognition}, volume={73}, number={2}, pages={85--92}, year={2010}, publisher={Elsevier}, comment={The tractography package used was 3D Slicer (www.slicer.org).} } @inproceedings{odonnell2010fiber, title={The fiber laterality histogram: a new way to measure white matter asymmetry}, author={O'Donnell, Lauren J and Westin, Carl-Fredrik and Norton, Isaiah and Whalen, Stephen and Rigolo, Laura and Propper, Ruth and Golby, Alexandra J}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={225--232}, year={2010}, organization={Springer}, comment={Whole brain tractography was generated by seeding trajectories (fibers) on a 2mm grid throughout the entire white matter of each subject using Runge-Kutta order two integration in 3D Slicer (www.slicer.org)} } @article{rathi2010tensor, title={Tensor kernels for simultaneous fiber model estimation and tractography}, author={Rathi, Yogesh and Malcolm, James G and Michailovich, Oleg and Westin, Carl-Fredrik and Shenton, Martha E and Bouix, Sylvain}, journal={Magnetic resonance in medicine}, volume={64}, number={1}, pages={138--148}, year={2010}, publisher={Wiley Online Library}, comment={Last, when performing tractography on real data, we use single- tensor streamline tractography as a baseline[Slicer].} } @article{malcolm2010filtered, title={A filtered approach to neural tractography using the Watson directional function}, author={Malcolm, James G and Michailovich, Oleg and Bouix, Sylvain and Westin, Carl-Fredrik and Shenton, Martha E and Rathi, Yogesh}, journal={Medical Image Analysis}, volume={14}, number={1}, pages={58--69}, year={2010}, publisher={Elsevier}, comment={Last, when performing tractography on real data, we use single-tensor streamline tractography as a baseline[Slicer]} } @article{voineskos2010diffusion, title={Diffusion tensor tractography findings in schizophrenia across the adult lifespan}, author={Voineskos, Aristotle N and Lobaugh, Nancy J and Bouix, Sylvain and Rajji, Tarek K and Miranda, Dielle and Kennedy, James L and Mulsant, Benoit H and Pollock, Bruce G and Shenton, Martha E}, journal={Brain}, volume={133}, number={5}, pages={1494?1504}, year={2010}, publisher={Oxford Univ Press}, comment={Tractography and creation of white matter fibre tracts were performed using 3D Slicer (http://www.slicer.org) and MATLAB 7.0 (http://www.mathworks.com).} } @article{kawashima2009uncinate, title={Uncinate fasciculus abnormalities in recent onset schizophrenia and affective psychosis: a diffusion tensor imaging study}, author={Kawashima, Toshiro and Nakamura, Motoaki and Bouix, Sylvain and Kubicki, Marek and Salisbury, Dean F and Westin, Carl-Fredrik and McCarley, Robert W and Shenton, Martha E}, journal={Schizophrenia research}, volume={110}, number={1}, pages={119--126}, year={2009}, publisher={Elsevier}, comment={After reconstruction, diffusion-weighted images were transferred to Linux workstations using medical imaging software (3D-Slicer version 2.8; an open source development project begun at the Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, U.S.A. and the Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital, Boston, MA, U.S.A.), on which eigenvalues, eigenvectors, mean diffusivity (Dm), and FA were calculated.} } @article{peng2009development, title={Development of a human brain diffusion tensor template}, author={Peng, Huiling and Orlichenko, Anton and Dawe, Robert J and Agam, Gady and Zhang, Shengwei and Arfanakis, Konstantinos}, journal={Neuroimage}, volume={46}, number={4}, pages={967--980}, year={2009}, publisher={Elsevier}, comment={ROIs were selected, which functioned as seeds for tractography based on the stream-lines approach with 2nd order Runge-Kutta integration (www.slicer.org).} } @article{lewis2009relation, title={The relation between connection length and degree of connectivity in young adults: a DTI analysis}, author={Lewis, John D and Theilmann, Rebecca J and Sereno, Martin I and Townsend, Jeanne}, journal={Cerebral Cortex}, volume={19}, number={3}, pages={554--562}, year={2009}, publisher={Oxford Univ Press}, comment={Using the 3D Slicer DTMRI module (an open source development project begun at the Massachusetts Institute of Technology Artificial Intelligence Laboratory and the Surgical Planning Laboratory at Brigham and Women's Hospital), the two 4-dimensional diffusion-weighted volumes were then converted to diffusion tensor volumes, coregistered using nonlinear tensor-to-tensor registration; Tracts were generated using a modified version of 3D Slicer, which allowed tracts to be terminated at the midsagittal point of the corpus callosum and to be filtered out if they terminated elsewhere.} } @inproceedings{oguz2009cortical, title={Cortical correspondence with probabilistic fiber connectivity}, author={Oguz, Ipek and Niethammer, Marc and Cates, Josh and Whitaker, Ross and Fletcher, Thomas and Vachet, Clement and Styner, Martin}, booktitle={International Conference on Information Processing in Medical Imaging}, pages={651--663}, year={2009}, organization={Springer}, comment={In this work, we use an open-source implementation of a modification of Friman's stochastic tractography algorithm[15]; We are thankful to Randy Gollub and the MIND Clinical Imaging Consortium for the data, and Tri Ngo, Carl-Fredrik Westin and Polina Golland for the stochastic tractography software implemented as a 3D Slicer module.} } @inproceedings{orban2009pilot, title={A pilot study of fMRI and fiber tracking to monitor effects of irradiation on brain tumour patients}, author={Orban de Xivry, Jonathan and Roelofs, Erik and Piccoli, Tommaso and Veninga, Theo and Goebel, Rainer and Di Salle, Francesco and Lambin, Philippe and Baumert, Brigitta}, booktitle={Fourth International Conference on Translational Research and Pre-Clinical Strategies in Radiation Oncology (ICTR)}, year={2009}, pages={NA}, comment={Tractography was operated on the diffusion tensor images to locate fibers around the tumour using 3D Slicer.} } @article{voineskos2009quantitative, title={Quantitative examination of a novel clustering method using magnetic resonance diffusion tensor tractography}, author={Voineskos, Aristotle N and O'Donnell, Lauren J and Lobaugh, Nancy J and Markant, Doug and Ameis, Stephanie H and Niethammer, Marc and Mulsant, Benoit H and Pollock, Bruce G and Kennedy, James L and Westin, Carl-Fredrik and Shenton, ME}, journal={Neuroimage}, volume={45}, number={2}, pages={370--376}, year={2009}, publisher={Elsevier}, comment={Tractography and creation of white matter fibre tracts using both the clustering and multiple region of interest approach were performed using 3D Slicer (open source software www.slicer.org) and Matlab 7.0.} } @inproceedings{malcolm2009neural, title={Neural tractography using an unscented Kalman filter}, author={Malcolm, James G and Shenton, Martha E and Rathi, Yogesh}, booktitle={International Conference on Information Processing in Medical Imaging}, pages={126--138}, year={2009}, organization={Springer}, comment={Last, when performing tractography on real data, we use single-tensor streamline tractography as a baseline[Slicer].} } @article{terry44white, title={White Matter Properties of Emotion Related Connections in Schizophrenia}, author={Terry, Douglas P and Rausch, Andrew C and Alvarado, Jorge L and Melonakos, Eric D and Markant, Doug and Westin, Carl-Fredrik and Kikinis, Ron and Von Siebenthal, Julien and Shenton, Martha E and Kubicki, Marek}, journal={Age}, volume={44}, number={43.00}, pages={0--65}, year={2009}, comment={Once ROIs were transferred to DTI space, stochastic tractography (http://www.slicer.org)) was performed to generate WM connections.} } @article{fitzsimmons2009diffusion, title={Diffusion tractography of the fornix in schizophrenia}, author={Fitzsimmons, J and Kubicki, M and Smith, K and Bushell, G and Estepar, R San Jose and Westin, Carl-Fredrik and Nestor, PG and Niznikiewicz, MA and Kikinis, R and McCarley, RW and Shenton, ME.}, journal={Schizophrenia research}, volume={107}, number={1}, pages={39--46}, year={2009}, publisher={Elsevier}, comment={Fornix extraction and measurements were obtained using 3Dslicer software (www.slicer.org) and diffusion tensor tractography.} } @phdthesis{maddah2008quantitative, title={Quantitative analysis of cerebral white matter anatomy from diffusion MRI}, author={Maddah, Mahnaz}, year={2008}, school={Massachusetts Institute of Technology}, comment={Manual outlining of ROIs for tractography was performed in 3D Slicer(www.slicer.org)} } @article{fjell2008relationship, title={The relationship between diffusion tensor imaging and volumetry as measures of white matter properties}, author={Fjell, Anders M and Westlye, Lars T and Greve, Doug N and Fischl, Bruce and Benner, Thomas and van der Kouwe, André JW and Salat, David and Bjornerud, Atle and Due-Tonnessen, Paulina and Walhovd, Kristine B}, journal={Neuroimage}, volume={42}, number={4}, pages={1654--1668}, year={2008}, publisher={Elsevier}, comment={3D slicer (http://www. slicer.org/) was used to create three dimensional renderings of the probabilistically defined tracts.} } @inproceedings{magnotta2008gtract, title={GTRACT: An Open Source Diffusion Tensor and Fiber Tracking Toolkit}, author={Magnotta, Vincent A and Harris, Greg and Ingalhalikar, Madhura and Tao, Xiaodong}, booktitle={MICCAI-CDMRI}, pages={208}, year={2008}, publisher={Citeseer}, comment={A graphical user interface to the tools is provided using the Slicer3 execution model. The tools support the NRRD image format and output tracts in VTK format which is supported by the NA-MIC toolkit and can be visualized in Slicer3.} } @book{banks2008global, title={Global illumination of white matter fibers from DT-MRI data}, author={Banks, David C and Westin, Carl-Fredrik}, booktitle={Visualization in Medicine and Life Sciences}, pages={173--184}, year={2008}, publisher={Springer}, comment={Visualization produced by 3D Slicer using local illumination.} } @inproceedings{maddah2008mathematical, title={A mathematical framework for incorporating anatomical knowledge in DT-MRI analysis}, author={Maddah, Mahnaz and Zollei, Lilla and Grimson, W Eric L and Westin, Carl-Fredrik and Wells, William M}, booktitle={IEEE International Symposium on Biomedical Imaging (ISBI)}, pages={105--108}, year={2008}, organization={IEEE}, comment={We use the atlas constructed by Mori et al. (http://lbam.med.jhmi.edu) which consists of 48 labeled regions that correspond to major anatomical bundles of fiber tracts in the human brain. Visualization of some of these regions in the 3D Slicer (www.slicer.org) is shown in Fig. 2.} } @article{pujol2008lowering, title={Lowering the barriers inherent in translating advances in neuroimage analysis to clinical research applications}, author={Pujol, Sonia and Kikinis, Ron and Gollub, Randy}, journal={Academic radiology}, volume={15}, number={1}, pages={114--118}, year={2008}, publisher={Elsevier}, comment={We analyzed selected exemplar datasets with the open-source 3DSlicer package developed by the NA-MIC consortium (15)} } @article{larsen2007quantitative, title={Quantitative comparison of functional MRI and direct electrocortical stimulation for functional mapping}, author={Larsen, S and Kikinis, R and Talos, I-F and Weinstein, D and Wells, W and Golby, A}, journal={The international journal of medical robotics+ computer assisted surgery: MRCAS}, volume={3}, number={3}, pages={262}, year={2007}, publisher={NIH Public Access}, comment={We obtained diffusion tracts using the 3D tractography method described by (8). This method is fully implemented in 3D-Slicer.} } @article{dauguet2007comparison, title={Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain}, author={Dauguet, Julien and Peled, Sharon and Berezovskii, Vladimir and Delzescaux, Thierry and Warfield, Simon K and Born, Richard and Westin, Carl-Fredrik}, journal={Neuroimage}, volume={37}, number={2}, pages={530--538}, year={2007}, publisher={Elsevier}, comment={We performed all tractography tests with the 3DSlicer toolkit and viewer (readily available at http://www.slicer.org).} } @article{talos2007volumetric, title={Volumetric assessment of tumor infiltration of adjacent white matter based on anatomic MRI and diffusion tensor tractography}, author={Talos, Ion-Florin and Zou, Kelly H and Kikinis, Ron and Jolesz, Ferenc A}, journal={Academic radiology}, volume={14}, number={4}, pages={431--436}, year={2007}, publisher={Elsevier}, comment={First, fractional anisotropy maps were generated in each case, using the 3D-Slicer software; For the 3D-tractography, we used the algorithm described by Westin et al. [24], which is fully implemented in the 3D-Slicer package.} } @inproceedings{estepar2006kernel, title={A kernel-based approach for user-guided fiber bundling using diffusion tensor data}, author={Estepar, Raul San Jose and Kubicki, Marek and Shenton, Martha and Westin, Carl-Fredrik}, booktitle={Annual International Conference of the IEEE Engineering in Medicine and Biology Society}, pages={2626--2629}, year={2006}, organization={IEEE}, comment={The tractography has been carried out using a hyperstreamline algorithm based on integrating the fiber trajectory along the PDD and implemented in the open source platform 3D Slicer.} } @article{mulkern2006complementary, title={Complementary aspects of diffusion imaging and fMRI; I: structure and function}, author={Mulkern, Robert V and Davis, Peter E and Haker, Steven J and Estepar, Raul San Jose and Panych, Lawrence P and Maier, Stephan E and Rivkin, Michael J}, journal={Magnetic resonance imaging}, volume={24}, number={4}, pages={463--474}, year={2006}, publisher={Elsevier}, comment={The tractography algorithm was implemented as part of the 3D Slicer package of the Surgical Planning Laboratory at the Brigham and Women's Hospital and used an FA cutoff value of 0.1.} } @article{shimony2006diffusion, title={Diffusion tensor imaging reveals white matter reorganization in early blind humans}, author={Shimony, JS and Burton, H and Epstein, AA and McLaren, DG and Sun, SW and Snyder, AZ}, journal={Cerebral Cortex}, volume={16}, number={11}, pages={1653--1661}, year={2006}, publisher={Oxford Univ Press}, comment={The tractography results obtained in all participants were inspected using 3D Slicer (http://www.slicer.org).} } @article{odonnell2006method, title={A method for clustering white matter fiber tracts}, author={O'Donnell, Lauren J and Kubicki, Marek and Shenton, Martha E and Dreusicke, Mark H and Grimson, W Eric L and Westin, Carl-Fredrik}, journal={American Journal of Neuroradiology}, volume={27}, number={5}, pages={1032--1036}, year={2006}, publisher={Am Soc Neuroradiology}, comment={Both of these analyses, tractography and fiber clustering, were performed using 3D Slicer software (www.slicer.org).} } @inproceedings{maddah2005automated, title={Automated atlas-based clustering of white matter fiber tracts from DTMRI}, author={Maddah, Mahnaz and Mewes, Andrea UJ and Haker, Steven and Grimson, W Eric L and Warfield, Simon K}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={188--195}, year={2005}, organization={Springer}, comment={The region of interests (ROIs) were outlined by an expert based on information from the map of the fractional anisotropy (FA), and a map, which color-codes the direction of the main eigenvector, both generated in the slicer.} } @inproceedings{talos2003diffusion, title={Diffusion tensor and functional MRI fusion with anatomical MRI for image-guided neurosurgery}, author={Talos, Ion-Florin and O'Donnell, Lauren J. and Westin, Carl-Fredrick and Warfield, Simon K and Wells III, William and Yoo, Seung-Schik and Panych, Lawrence P and Golby, Alexandra and Mamata, Hatsuho and Maier, Stefan S and Ratiu, Peter and Guttmann, Charles R. G. and Black, Peter M. and Jolesz, Ferenc A. and Kikinis, Ron}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={407--415}, year={2003}, organization={Springer} } @inproceedings{odonnell2005white, title={White matter tract clustering and correspondence in populations}, author={O'Donnell, Lauren J. and Westin, Carl-Fredrik}, booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention}, pages={140--147}, year={2005}, organization={Springer} } @article{goldberg2005diffusion, title={Diffusion tensor magnetic resonance imaging in multiple sclerosis}, author={Goldberg-Zimring, Daniel and Mewes, Andrea UJ and Maddah, Mahnaz and Warfield, Simon K}, journal={Journal of Neuroimaging}, volume={15}, number={s4}, pages={68S--81S}, year={2005}, publisher={Wiley Online Library} } @article{kubicki2005application, title={The application of DTI to investigate white matter abnormalities in schizophrenia}, author={Kubicki, Marek and Westin, Carl-Fredrik and McCARLEY, ROBERT W and Shenton, Martha E}, journal={Annals of the New York Academy of Sciences}, volume={1064}, number={1}, pages={134--148}, year={2005}, publisher={Wiley Online Library} } @article{berman2004diffusion, title={Diffusion-tensor imaging-guided tracking of fibers of the pyramidal tract combined with intraoperative cortical stimulation mapping in patients with gliomas}, author={Berman, Jeffrey I and Berger, Mitchel S and Mukherjee, Pratik and Henry, Roland G}, journal={Journal of neurosurgery}, volume={101}, number={1}, pages={66--72}, year={2004}, publisher={Journal of Neurosurgery Publishing Group} } @article{park2004method, title={Method for combining information from white matter fiber tracking and gray matter parcellation}, author={Park, Hae-Jeong and Kubicki, Marek and Westin, Carl-Fredrik and Talos, Ion-Florin and Brun, Anders and Peiper, Steve and Kikinis, Ron and Jolesz, Ference A and McCarley, Robert W and Shenton, Martha E}, journal={American Journal of Neuroradiology}, volume={25}, number={8}, pages={1318--1324}, year={2004}, publisher={Am Soc Neuroradiology} } @phdthesis{larsen2003quantitative, title={Quantitative comparison of functional MRI and electro-cortical stimulation for function mapping}, author={Larsen, Sara E}, year={2003}, school={Massachusetts Institute of Technology} } @book{talos2003magnetic, title={Magnetic Resonance Imaging-Guided Stereotactic Biopsy in the Central Nervous System}, author={Talos, Ion-Florin and Black, Peter M}, booktitle={Image-Guided Diagnosis and Treatment of Cancer}, pages={101--115}, year={2003}, publisher={Springer} } @inproceedings{brun2003coloring, title={Coloring of DT-MRI fiber traces using Laplacian eigenmaps}, author={Brun, Anders and Park, Hae-Jeong and Knutsson, Hans and Westin, Carl-Fredrik}, booktitle={International conference on computer aided systems theory}, pages={518--529}, year={2003}, organization={Springer} } @article{hodaie2010vivo, title={In Vivo Visualization of Cranial Nerve Pathways in Humans Using Diffusion-Based Tractography}, author={Hodaie, Mojgan and Quan, Jessica and Chen, David Qixiang}, journal={Neurosurgery}, volume={66}, number={4}, pages={788--796}, year={2010}, publisher={LWW} } @article{archip2007non, title={Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery}, author={Archip, Neculai and Clatz, Olivier and Whalen, Stephen and Kacher, Dan and Fedorov, Andriy and Kot, Andriy and Chrisochoides, Nikos and Jolesz, Ferenc and Golby, Alexandra and Black, Peter M and Simon, K. Warfield}, journal={Neuroimage}, volume={35}, number={2}, pages={609--624}, year={2007}, publisher={Elsevier} }