In this blog post, I want to share my thoughts on the number of layers that should be extracted from any given dataset. I will try to give an overview of how many layers are usually extracted in the field, I’ll describe my personal choices of layer numbers, and I will try to discuss the challenges of layer signal extraction along the way.
In this blog post Sri Kashyap and I describe how to deal with the registration of high-resolution datasets across days, across different resolutions, and across different sequences.
I am particularly fond of the following two tools: Firstly, ITK-SNAP for visually-guided manual alignment and secondly, using ANTs programs: antsRegistration and antsApplyTransforms.
Maximum intensity projection and minimum intensity projection can be insightful for mapping of vessels in 3D-slabs. In this post, I describe the application of intensity projections with LAYNII.
CBV-fMRI with VASO is highly dependent on a good inversion contrast. It gives it its CBV sensitivity and is also responsible for most of the VASO specific pitfalls (e.g. inflow, CSF etc. ). And thus, it should be optimized as much as possible.
In this blog post, I want to describe the most important features of a reliable inversion pulse for the application of VASO at 7T with a head transmit coil.
Continue reading “TR-FOCI pulse optimisations for SS-SI VASO”
ISIS-conv is a very useful dicom to nii converter from Enrico Reimer. ISIS-conv gets along with a lot of challenging data sets that no other converter (that I know of) can handle so conveniently:
There is a Mac-installation package of ISIS-conv. Unfortunately, however, with every IOS update, it has become more complicated to install it.
Since, I spend too much time figuring out how to install it after every update, I am collecting the necessary steps in this Blog post for future reference:
In this blog post, I want to describe the application and working principle of a few spatial smoothing algorithms that are implemented in LAYNII.
LN_GRADSMOOTHLN_LAYERSMOOTHLN_LAYERSMOOTHLN_DIRECT_SMOOTHLN_TEMPSMOOTHThe following is a list of my favorite layer-fMRI abstracts at SFN in San Diego.
Continue reading “Layer-fMRI abstracts at SFN 2018 in San Diego”
