Processing requiring nonlinear optimization, signal processing, image manipulations, or DICOM reading/writing will require installation of additional toolboxes. There are numerous publicly shared, open-source MRI processing code written on the MATLAB platform which can be directly ported to the open source platform GNU Octave. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure, which are part of this book. In general, the nuances of hyperpolarized MRI may complicate image processing and could potentially bias parameters that are calculated from images if not properly taken into account. Furthermore, it is extremely difficult to map out the transmitter profile due to the low natural 13C abundance in vivo. For instance, although precise flip angle knowledge is key to the estimation of virtually every parameter measured here, θ is typically estimated using an external reference phantomĭuring imaging. However, a thorough error propagation of parameter estimation is extremely difficult as is the estimation of all ancillary parameters influencing the measurements. In some of the subsequent examples of this chapter, this effect is accounted for, or it may be compensated for through the use of acquisition-based signal compensation. In addition to potentially degrading image resolution, this window has the consequence that physiological parameters calculated from the time course of image pixel intensity may be biased, either by RF flip angle ( θ) nonuniformity or by influence of relaxation times which are almost never known precisely beforehand in vivo. Instead, T 1 relaxation imposes an exponential decay envelope which decreases the z polarization over time. Image encoding requires radio frequency (RF) excitation of z polarization that is typically nonrenewable, meaning it does not recover with T 1 relaxation. One of the primary differences is the constant depolarization of the contrast agent during imaging. We select a few applications which will be interesting for researchers studying renal physiology and function in a preclinical setting, and where available, we point to links to source code for image processing pipelines.īeginning at the steps of image formation, there are some key attributes differentiating hyperpolarized from conventional MRI. Instead, we describe some of the applications more specific to hyperpolarized 13C data analysis, and we guide the reader through details and attempt to point out pitfalls. are nearly identical and will not be discussed in detail here. In general, much of the image-formation pipelines are nearly identical to those for 1H MRI particularly, the steps of Fourier transforming k-space data, reconstructing under-sampled data using parallel imaging afforded by RF coil arrays, etc. The choice of analysis strategy depends on numerous factors, including the imaging agent, the organ of interest, the acquisition strategy, and imaging parameter being measured. I found the same with the llvm-3.1 package.Can yield a wide variety of metabolic, structural, and functional information which is extracted via analysis of time-varying NMR signals. sudo port install ntfs-3g then finds the file i have downloaded and does not try to download it again. To achieve the same result, I downloaded and put it in /opt/local/var/macports/incoming/verified. opt/local/var/macports/distfiles/ntfs-3g/ntfs-3g_ntfsprogs-2012.1.15.tgz The port distfiles ntfs-3g gives me -> Distfiles for ntfs-3g Make sure that you have all the distfiles belonging to a given port as many ports have more than one. Proceed to install using sudo port install octave. Put the downloaded source package in that folder. Go to /opt/local/var/macports/distfiles and create a directory called octave if it doesn't exist. The links below that are a number of mirrors you could download from using your download manager. Inside the square brackets is the name of the file to download, followed by the path that MacPorts will search for the file. opt/local/var/macports/distfiles/octave/octave-3.2.4.tar.gz You'll get the following output: -> Distfiles for octave List the distfiles required for the port by running port distfiles octave. For test purposes, I'll use the octave port.
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