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Browsing by Author "Halkoaho, Johannes"

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  • Determining the partial volumes of brain tissue from spectroscopy voxels 
    Halkoaho, Johannes (2022)
    MRS or magnetic resonance spectroscopy is an imagining technique which can be used to gain information about the metabolite concentration within a certain volume of interest. This can be used for example in brain imagining. The brain consists of three main types of tissue: cerebrospinal fluid, white and gray matter. It is important to know the different volume fractions of these tissues as the resolution in MRS is significantly lower than that of magnetic resonance imagining (MRI). The tissues all have different metabolite profiles and in order to get meaningful data the volume fractions need to be taken into account. This information can be gained from the segmentation of an image formed by using MRI. In this work a software tool was created to find these volume fractions with the input of a .rda file that is created by the scanner and Nifti file. The Nifti file is the image formed by using MRI and the .rda file is the manufacturers raw data format for spectroscopy data which has the relevant information about the volumes of interest. The software tool was created using Python and JavaScript programming languages and different functions of FSL. FSL is a comprehensive library of analysis tools used in brain imaging data processing. The steps for the software tool are: determining the coordinates of the volume of interest in FSL voxel coordinates, creating a mask in the correct orientation and location, removing non-brain tissue from the image using FSL’s tool tailored for that purpose (BET), segmenting the image using FSL’s segmenting tool (FAST), registering the mask on the segmented images and calculating the volume fractions. The software tool was tested on imaging data that was obtained at Meilahti Kolmiosairaala for the purpose of the testing. The testing data set included five different spectroscopy volumes from different parts of the brain and a T1 weighted image. The software tool was given the relevant information about the volume of interest in the form of a .rda file and the T1 weighted image in the form of a Nifti file. The software tool then determined the different volume fractions from all of the five volumes of interest. There is variation on the volume fraction of different brain areas within different brains and it is not possible to have an absolute reference value. The results of the test corresponded to the possible volume fractions that can be expected from the volumes in question.
  • Primordial black holes and gravitational waves from inflation 
    Halkoaho, Johannes (2022)
    The primordial perturbations created by inflation in the early Universe are known to be able to produce significant amount of primordial black holes and gravitational waves with large amplitudes in some inflationary models. Primordial black holes are produced by primordial scalar perturbations and gravitational waves are partly primordial tensor perturbations and partly produced by scalar perturbations. In this thesis we review some of the current literature on the subject and discuss a few inflationary models that are capable of producing primordial scalar perturbations large enough to create a significant amount of primordial black holes. The main focus is on ultra-slow roll inflation with a concrete example potential illustrating the dynamics of the scenario followed by a briefer treatment of some of the alternative models. We start by explaining the necessary background theory for the understanding of the subject at hand. Then we move on to the inflationary models covered in this thesis. After that we explain the production of the primordial black holes and gravitational waves from scalar perturbations. Then we consider primordial black holes as a dark matter candidate and go through the most significant known restrictions on the existence of primordial black holes with different masses. We discuss some of the possible future constraints for the remaining possible mass window for which primordial black holes could explain all of dark matter. We then briefly discuss two planned space-based gravitational wave detectors that may be able to detect gravitational waves created by inflation.

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