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Background and purpose A novel method of retrospective liver modeling was developed based on four-dimensional magnetic resonance (4D-MR) images. The 4D-MR images will be utilized in generation of the subject-specific deformable liver model to be used in radiotherapy planning (RTP). The purpose of this study was to test and validate the developed 4D-magnetic resonance imaging (MRI) method with extensive phantom tests. We also aimed to build a motion model with image registration methods from liver simulating phantom images. Materials and methods A deformable phantom was constructed by combining deformable tissue-equivalent material and a programmable 4D CIRS-platform. The phantom was imaged in 1.5 T MRI scanner with T2-weighted 4D SSFSE and T1-weighted Ax dual-echo Dixon SPGR sequences, and in computed tomography (CT). In addition, geometric distortion of the 4D sequence was measured with a GRADE phantom. The motion model was developed; the phases of the 4D-MRI were used as surrogate data, and displacement vector fields (DVF's) were used as a motion measurement. The motion model and the developed 4D-MRI method were evaluated and validated with extensive tests. Result The 4D-MRI method enabled an accuracy of 2 mm using our deformable phantom compared to the 4D-CT. Results showed a mean accuracy of

Additional file 1: Detailed information on the datasets used in the study is given and optimization process of the baseline algorithms is described.

Purpose Methods and Materials Results Conclusions, Purpose: To study the registration accuracy in neck area when two consecutive CT studies are registered Difficulties in image registration are mostly due to non-rigidity of head and neck entity How large are the registration errors when rigid body model and...

Ischemic stroke is the most common cerebrovascular disease, and its diagnosis, treatment, and study relies on non-invasive imaging. Algorithms for stroke lesion segmentation from magnetic resonance imaging (MRI) volumes are intensely researched, but the reported results are largely incomparable due to different datasets and evaluation schemes. We approached this urgent problem of comparability with the Ischemic Stroke Lesion Segmentation (ISLES) challenge organized in conjunction with the MICCAI 2015 conference. In this paper we propose a common evaluation framework, describe the publicly available datasets, and present the results of the two sub-challenges: Sub-Acute Stroke Lesion Segmentation (SISS) and Stroke Perfusion Estimation (SPES). A total of 16 research groups participated with a wide range of state-of-the-art automatic segmentation algorithms. A thorough analysis of the obtained data enables a critical evaluation of the current state-of-the-art, recommendations for further developments, and the identification of remaining challenges. The segmentation of acute perfusion lesions addressed in SPES was found to be feasible. However, algorithms applied to sub-acute lesion segmentation in SISS still lack accuracy. Overall, no algorithmic characteristic of any method was found to perform superior to the others. Instead, the characteristics of stroke lesion appearances, their evolution, and the observed challenges should be studied in detail. The annotated ISLES image datasets continue to be publicly available through an online evaluation system to serve as an ongoing benchmarking resource (www.isles-challenge.org).

Purpose and background In external beam radiotherapy (EBRT), the radiation is targeted from linear accelerator to cancerous tumors as a local treatment. The EBRT requires high accuracy for the whole process through the patient care path from medical imaging with irradiation units to linear accelerators. The dose uncertainty of the whole EBRT process must be less than five percent. [ICRU (1976)] Radiotherapy planning (RTP) considers patient anatomy, target volume (tumor + preferred safety margins), organs-at-risk (OAR), integral body dose and prescribed dose to target volume by optimizing the best possible compromise dose distribution with the simplest technical solutions. Magnetic resonance imaging (MRI) is increasingly used in RTP since it has superior soft-tissue contrast compared to Computed Tomography (CT). Therefore, MRI is utilized for visualization of soft tissue tumors (or lesions), for example in the liver area. However, uncertainties such as geometrical distortions and motion artefacts may have reduced the clinical value of the MRI data. An inaccurate dose in target volumes and/or OAR can lead to an undesired clinical response. The four-dimensional (4D) imaging visualizes the motion of tissue volume and is used: to define comprehensive margins to EBRT or suitable respiratory phase to give radiotherapy, or to indicate the tumor position for image guided radiotherapy. Liver motion is mainly caused by respiration, peristaltic and cardiac motion. The 4D images can be used to build a liver motion model which can be utilized when liver motion cannot be tracked, or the motion is invisible with sufficient spatial resolution and/or contrast. The main goal of the thesis was to improve the accuracy of MRI in liver radiotherapy. The purpose was to study the geometrical accuracy of several MRI scanners used in RTP, and to suggest geometrical accuracy acceptance criteria for the scanners. The purpose was to develop a 4D-MRI method for the liver and create a clinical procedure with acceptable imaging time, and sufficient temporal and spatial accuracy. The aim was to build a motion model with image registration methods from liver-simulating phantom images. Finally, the aim was to test and validate the developed methods with phantom tests. Method and results Geometrical accuracy was studied at five different MRI scanners used in radiotherapy clinics with three different sequences using commercial large field-of-view phantom. For all scanners and sequences except one, the mean and median distortion magnitude was

Individually navigated transcranial magnetic stimulation (nTMS) has been used to locate and map the primary motor cortical areas since the inception of the technique. Recently, it has been added to the pre-surgical routine for epilepsy and brain tumor patients. The accuracy of the mappings in healthy volunteers and brain tumor patients and their feasibility in the pre-surgical evaluation of brain tumor patients have been established. The originating causes for epilepsy are variable and affect the functional localizations in relation to conventional anatomy. A reliable and versatile pre-surgical method for the localization of the functional cortical areas is essential for pre-surgical risk-benefit assessments and it is important to the success of surgical treatments. In this thesis, I describe an nTMS mapping protocol suitable for clinical use and evaluate the accuracy of the motor cortical mappings by comparing the results with the results of direct electrical stimulation of the primary motor cortex. The accuracy, 11 ± 4 mm for the hand and 16 ± 7 mm for the arm muscle groups, is sufficiently good for pre-surgical evaluation in patients with severe epilepsy. With this patient group, the nTMS technique enables the mapping of the abnormally excitable tissue, which has an impact on the interpretation and reliability of the mappings as well. In addition to the mapping of the motor cortical areas, the cortical areas related to speech are of key interest in neurosurgery. The speech-related cortical areas are commonly localized noninvasively with functional magnetic resonance imaging techniques. The dominant hemisphere for language functions can be discriminated with the invasive Wada test in the pre- surgical evaluation of epilepsy patients. Recently, nTMS protocols have been introduced for localization of speech-related cortical areas. The analysis of the nTMS elicited modifications in the language task performance have commonly been analyzed manually from video recordings and the methods for the reliable determination of the nTMS elicited speech-response latencies, their categorization and analysis, have been sparse. In the last part of this dissertation, I developed a semi-automated script for the speech-response latency difference calculation based on the accelerometer signal of the speech-response elicited vibrations of the larynx. The developed script was individually optimized for speech-response detection. According to the presented results the method is capable of determining the speech-response latencies with a sensitivity of 96% and a specificity of 71%, against the manual review from the video and visual observations from the accelerometer signals. Based on the results presented in this thesis, nTMS is a reliable method for the mapping of the functional cortical areas pre-surgically in patients with severe epilepsy. It also enables the mapping of abnormally excitable brain areas. Yksilöllisesti navigoitua transkraniaalista magneettistimulaatiota (nTMS) on käytetty koko menetelmän olemassaolon ajan liikeaivokuoren tarkkaan paikantamiseen, ja viime vuosina menetelmää on ryhdytty käyttämään rutiininomaisesti ennen kirurgista hoitoa epilepsia- ja aivokasvainpotilailla. nTMS-kartoitusten luotettavuus terveillä koehenkilöillä on vakiintunut ja kartoitusten on todettu olevan käyttökelpoisia aivokasvainpotilailla leikkaushoidon suunnittelussa. Vaikeaa epilepsiaa sairastavilla potilailla kohtausten alkusyy voi vaihdella suuresti, millä voi olla vaikutusta aivokuoren toiminnallisten alueiden sijaintiin suhteessa tavanomaiseen anatomiaan. Riittävän monipuolinen ja luotettava toiminnallisten alueiden kartoitus ennen leikkauksen riski-hyötyarviointia ja leikkauspäätöstä on hyödyllistä hoidon onnistumisen kannalta. Tässä väitöskirjatyössä esittelen kliiniseen työhön soveltuvan epilepsiapotilaiden liikeaivokuoren paikannusprotokollan ja osoitan protokollalla saatujen nTMS-kartoitustulosten tarkkuuden vastaavan aivokuoren pinnalta tehtyjen suorien sähköstimulaatioiden tuloksia. Menetelmän tarkkuuden voidaan todeta olevan riittävä leikkaushoidon suunnitteluun vaikeaa epilepsiaa sairastavilla potilailla. nTMS-menetelmällä on mahdollista paikantaa myös epilepsiaa sairastavien potilaiden poikkeavasti ärtyviä aivokuoren alueita. Tällä on merkitystä kartoitustuloksia tulkittaessa ja niiden luotettavuutta arvioitaessa, samoin kuin kirurgisesti poistettavan alueen laajuutta ja kohdennusta määritettäessä. Epilepsiaa sairastavien potilaiden liikeaivokuoren paikantamisen lisäksi mielenkiinnon kohteena on puheen tuottamiseen ja käsittelyyn liittyvien aivokuorialueiden paikannus. Näitä aivokuoren alueita paikannetaan tyypillisesti toiminnallisella magneettikuvantamisella. Leikkaushoitoa suunniteltaessa kielellisiä alueita hallitseva aivopuolisko voidaan erottaa myös Wada-testin avulla. Sarjoittaista nTMS menetelmää hyödyntäviä kielellisten alueiden paikannusprotokollia on kehitetty, mutta niissä stimulaation aiheuttamia muutoksia potilaan suoriutumiseen annetusta tehtävästä on tyypillisesti voitu analysoida vain videotallenteita katsomalla. Erityisesti saatujen puhevasteiden toistettavaan ja objektiiviseen luokitteluun ja analyysiin on ollut tarjolla vain vähän menetelmiä. Analyysin helpottamiseksi kehitin kiihtyvyysanturisignaaliin perustuvan yksilöllisesti optimoidun puoliautomaattisen analysointirutiinin puhevasteiden viive-erojen määritykseen. Tulosten mukaan analysointirutiinin suorituskyky puhevasteiden viiveiden tunnistuksessa oli hyvä (sensitiivisyys 96 % ja spesifisyys 71 % verrattuna manuaaliseen analyysiin videolta ja suoraan signaalista). Väitöskirjassa esitettyjen tulosten perusteella voidaan todeta nTMS-menetelmän olevan käyttökelpoinen ja luotettava tutkimusmenetelmä vaikeaa epilepsiaa sairastavien potilaiden leikkausta edeltävään toiminnallisten alueiden kartoitukseen. nTMS-menetelmällä voidaan saada myös lisätietoa poikkeavan herkästi ärtyvistä aivoalueista.