This post summarizes the presentation, tutorials, and discussions of the 2019 UHF Minnesota Workshop on Cortical Depth-Resolved fMRI Methods, Nov 12th-Nov 13th.
Author: renzohuber
Layer-fMRI Jobs
This page lists all open layer-fMRI job opportunities.
Suggestions are welcome to layerfMRI@gmail.com
- 2023 Post Doc with possible layer-fMRI focus at Nijmegen with Jose Marques and David Norris.
- 2023 Senior Lecturer on Development and aging at the 7T layer-fMRI focused center in Glasgow.
- 2023 Post-doc position on layer-fMRI methods in Baltimore, USA with Jun Hua.
- 2022 Post-doc position on UHF high-resolution (f)MRI methods, Boston USA with Anna Blazejewska.
- 2022 PhD position on Laminar specific simultaneous Electroencephalography and Functional Magnetic Resonance Imaging in Epilepsy, At Kings college London, UK.
- 2022 PhD position opening on layer fMRI of prefrontal cortex at Roshan Cools lab in Nijmegen (Donders), Netherlands.
- 2022 PhD student position on layer-fMRI for surface perception. with Peter de Weerd, Maastricht Netherlands.
- 2022 PhD student Position on time resolved decoding and layer-fMRI with Peter Kok at UCL, London, UK.
- 2022 Staff scientists for NIH core facility that manages two 7Ts, Bethesda with Peter Bandettini.
- 2022 Fellow/senior researcher to work on 7T MRI tools, in Queensland Australia with Markus Barth.
- 2022 Postdoc position in Geneva starting in May 2022 with Olivier Reynaud on MRI methods development including layer-fMRI at their new 7T.
- 2022 Research Fellow at UCL (London) for 7T methods development with Guillaume Flandin(closing date is 30th April).
- 2021 Post doc postion with Floris de Lange in Nijmegen on Laminar Computations of Sensory Surprise.
- 2021 2 positions available at UC Berkeley / AMRIT with the NexGen 7T with David Feinberg: postdoc and a pulse sequence programmer.
- 2021 Assistant Researcher position to work on the Feinbergatron scanner in Berkeley, a 7T scanner build for the purpose of human layer-fMRI.
- 2021 Layer-fMRI post doc position on Cognitive Dopamine Function in Nijmegen, with Roshan Cools.
- 2021 Two post-doc positions on human layer-fMRI signal investigation and modeling at MGH with Jonathan Polimeni. [Post 1] and [Post 2].
- 2021 Max-Planck research group leader position (W2) on human layer-fMRI in Tuebingen Germany with Klaus Scheffler. And another one on animal models [here].
- 2021 PhD position available (now also for international students) from July 2022, in Queensland (AUS) with Markus Barth.
- 2021 A two year post-doc position available in Essen to work with the group of Nikolai Axmacher on laminar fMRI of the hippocampus. Deadline Oct 15th 2021.
- 2021 Two PhD positions on layer-(f)MRI with Markus Barth in Queensland, Australia. Deadline Aug 23rd 2021.
- 2021 Tenure research position on fMRI at ultra-high-fields with Nicolas Boulant, at Neurospin near Paris.
- 2021 Post-Doc for layer-fMRI, in the Section of Functional imaging methods with Peter Bandettini, at NIH, Bethesda, USA.
- 2021 Research Scientists and/or Postdoctoral Researchers Position at the Laboratory for Consciousness (Hakwan Lau), in Riken Japan.
- 2021 PostDoc position to form om laminar-fMRI and EEG human fear extinction learning in Dortmund with Erhan Genç.
- 2021 Two PhD positions on layer-fMRI regarding auditory neuroscience with Federico De Martino in Maastricht.
- 2021 A PostDoc position on high resolution fMRI in non-human primates with Qi Zhu at NeuroSpin.
- 2021 A PostDoc position on laminar fMRI examining the role of feedback in human visual perception at the MPI in Tuebingen, Germany. (with Kiley Seymour)
- 2021 A Postdoc and a PhD position on mesoscale imaging in Magdeburg, Germany (Esther Kuehn)
- 2021 Two Postdoc positions for (layer-fMRI) methods development at UCL, UK, (Guillaume Flandin)
- 2020 Head of Imaging Core Facility in Juelich (with new 7T Terra scanner), Germany (ask Prof Weiss-Blankenhorn p.h.weiss@fz-juelich.de for more information).
- 2020 Open Rank position in Illinois to work with a new 7T Terra system (Brad Sutton bsutton@illinois.edu for more information).
- 2020 PhD position in Leipzig and Juelich on high resolution functional connectivity at 7T with Sofie Valk.
- 2020 Vadim Axelrod will host a postdoc for 7T layer-fMRI research in Israel. Applicable for PhD graduates from EU countries and Canada. vadim.axelrod@gmail.com
- 2020 3 Post doc positions at Freie Universitaet Berlin, on layer-fMRI. As part of ERC grant awarded to Radek Cichy.
- 2020 Faculty position for 7T in RIKEN (Japan)
- 2020 PhD student position to work in Maastricht with Federiko DeMartino on layer-fMRI in the auditory cortex.
- 2020 Post Doc or Pre Doc position at UCL with Callaghan, Nadine Grädel, Nadège Corbin, and Ali Aghaeifar on MRI methods, including layer-fMRI with VASO.
- 2020 Post Doc position in Leipzig (Max-Planck) on layer-specific real-time fMRI with Nick Weiskopf and Romy Lorenz.
- 2020 Post Doc position in Liege (Belgium) on high-resolution fMRI with Eveline Balteau and Christophe Phillips.
- 2020 Post Doc position in the new lab from Kawin Setsompop in Stanford US, on advanced (f) MRI acquisition and reconstruction. Also in collaboration with the Feinbergatron layer-scanner in Berkeley.
- 2020 Staff scientist position in the new lab from Kawin Setsompop in Stanford US, on advanced (f) MRI acquisition and reconstruction. Also in collaboration with the Feinbergatron layer-scanner in Berkeley.
- 2020 PhD position for layer fMRI in Maastricht with Rainer Goebel (Brain Innovations) and Renzo Huber.
- 2020 Post-doc on high-resolution fMRI at 7T with Alexander Puckett at the University of Queensland, Australia
- 2020 Layer-fMRI postdoc, with Nikolai Axmacher at Ruhr University Bochum
- 2020 Layer-fMRI postdoc, with Blake Butler, in London Ontario
- 2020 Lausanne, Switzerland, with Ileana Jelescu on diffusion functional fMRI at 7T
- 2020 Brisbane, Australia, with Alex Puckett, Post-doc and PhD positions, on layer-fMRI
- 2020 Trondheim, in Systems Neuroscience, Faculty Associate Professor with 7T
- 2020 Glasgow, with Jozien Goense on layer-fMRI applications, two post-docs and a faculty position.
- 2019 Suwon, Korea, with Kamil Uludag, Post-doc position on layer-fMRI methods.
- 2019 The Veterans Health Research Institute, with An Vu, about microscale fMRI
- 2019 Maastricht, with Benedikt Poser, Post-doc, on UHF advanced imaging.
- 2019 Glasgow, with Lars Muckli, on layerfMRI and computational modeling
- 2019 Magdeburg, with layerfMRI-expert Esther Kuehn, PdH-Position on Neuronal Mechanisms of Autosuggestion
- 2019 NIH, Bethesda, with Peter Bandettini, multiple positions on fMRI methods, including layerfMRI.
- 2019 UCSF, with Duan Xu, on advances imaging methods at with a GE 7T scanner, Post-doc position.
- 2019 Aalto, Finland, Faculty position on NeuroImaging (7T Terra might come soon).
- 2019 Montreal, with Rick Hoge at their new 7T Terra, Research Associate position on advanced UHF functional imaging.
- 2019 Liege, with 7T Terra, Post-doc MRI physicist
- 2019 Maastricht, with Federiko de Martino, on layer-fMRI, Post-doc
Tutorial on scanning high-resolution EPI on SIEMENS scanners
This post lists the background material of the hands-on tutorial about high-resolution EPI on SIEMENS scanners.
Continue reading “Tutorial on scanning high-resolution EPI on SIEMENS scanners”
layer-fMRI abstracts
The following is a personal selection of my must-see layer-fMRI abstracts presented at SFN/OHBM/ISMRM. If I missed something, please let us know (layerfMRI@gmail.com).
SFN 2019 in Chicago
Saturday
- 4:00 pm – 5:00 pm, 092.12/ BB63. Poster, O. STANLEY, Phase-based macrovascular filtering from gradient echo bold fMRI reduces orientation dependence.
Sunday
- 8:00 am – 8:15 am, 111.01/Room S402. Nanosymposium talk, J. TOWNSEND: Non-invasive mapping of acoustic-phonetic speech features in human superior temporal gyrus using ultra-high field 7T fMRI.
- 11:00 am – 12:00 am, 141.04/K28. Poster, T. LIU: Affective processing of face stimuli in human primary visual cortex.
MP2RAGE: challenges and artifacts of its use for layer-fMRI
The MP2RAGE sequence is very popular for 7T anatomical imaging and is very commonly used to acquire 0.7-1 mm resolution whole brain anatomical reference data. Aside of this common application, it can also be very helpful for layer-fMRI studies to obtain even higher resolution T1 maps in the range of 0.5mm iso. However, when optimizing MP2RAGE sequence parameters for layer-fMRI studies, there are a few things that might be helpful to keep in mind.
In this post, I would like to discuss the challenges of using the popular MP2RAGE sequence in layer-fMRI studies. Specifically I will discuss challenges/features regarding:
- Background noise.
- Foldover artifact at very high resolutions.
- Usage of double-partial Fourier imaging.
- Inflow into arterial vessels.
Continue reading “MP2RAGE: challenges and artifacts of its use for layer-fMRI”
Example analysis pipeline of layer-VASO
In this blog post I want to go through the analysis pipeline of layer-dependent VASO.
I will go through the all the analysis steps that need to be done to go from raw data from the scanner to final layer profiles. The entire thing will take about 30 min (10 min analysis and 20 min explaining and browsing through data).
During the entire analysis pipeline I am using the following software packages: SPM, AFNI, and LAYNII, and gnuplot (if you want fancier plotting tools)
How many layers should I extract?
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.
‘layer fMRI’, ‘sub-millimeter fMRI’, ‘mesoscopic fMRI’, or ‘cortical depth dependent fMRI’…. Which term should I use?
What’s the best name of our field and what’s the best attributing term for our data? There are many competing options: “Layer fMRI”, “mesoscopic fMRI”, “sub-millimeter fMRI”, “ultra-high resolution fMRI”, “laminar fMRI”, “cortical depth-dependent fMRI”. They differ with respect to how flashy they are, how scientifically appropriate they are, and how popular they are.
In this blog post, I want to review which ones are the most popular ones in the field and also share some thoughts on my favourite candidates.
Edits on March 3rd 2019 with contributions and clarifications taken from Kamil Uludağ, Sri Kashyap and Faruk Gulban.
Registration of high-resolution data
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.
Intensity projections in LAYNII
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.
TR-FOCI pulse optimisations for SS-SI VASO
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”
Installing ISIS-conv on MAC
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:
- SMS-data, where individual slices have a non-constant inter-slice distances.
- VASO data with non-constant TRs
- Multi-echo, multi-coil, and Magnitude/Phase data.
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:
Continue reading “Installing ISIS-conv on MAC”Anatomically informed spatial smoothing
In this blog post, I want to describe the application and working principle of a few spatial smoothing algorithms that are implemented in LAYNII.
- Confined smoothing along similar anatomical structures with
LN_GRADSMOOTH - Smoothing along the layers with
LN_LAYERSMOOTH - Smoothing within columns with
LN_LAYERSMOOTH - Smoothing across specific spatial dimensions only with
LN_DIRECT_SMOOTH - Smoothing long the time domain with
LN_TEMPSMOOTH
Quick example of cortical unfolding in LAYNII
Update June 2021: There is a new and more comprehensive 3D-supported LayNii Program for cortical unfolding. Please see https://thingsonthings.org/ln2_multilaterate/
The blog post below is kept for archiving purposes:
In this Blog post, I seek to describe a quick example of how to analyse high-resolution data across layers and columns with LAYNII.
Continue reading “Quick example of cortical unfolding in LAYNII”
Negative Voxels in VASO
In the last years, I and multiple other VASO users have encountered many occasions of voxels that show negative CBV change (positive VASO signal change) while the BOLD suggests that the activation should be positive. In this blog post, I want to list potential sources of this surprising effect.
How send raw k-space data to any given server with Twix or with a modified ICE-chain
In this blog-post I want to describe a setup, how you can include an additional ICE functor in your reconstruction pipeline that sends raw Twix files from the Reconstruction computer to any given custom server. Continue reading “How send raw k-space data to any given server with Twix or with a modified ICE-chain”
List of potential layer-fMRI application studies
Recently, my adviser Peter Bandettini asked me to compile a list of all potential applications for layer-fMRI. It was a fun exercise to think about it. Below, you find a list of all potential applications that I could think of. Continue reading “List of potential layer-fMRI application studies”
How to install nifty QuickLook
In this blogpost I describe how to install the DTI-TK NIfTI quicklook plugin for nii files for mac OS.
3D-printing nii data
In this blog post, I want to write about pipelines on how to prepare Nifti-brain data and make them printable by a 3D-printer.
Two pipelines are shown. One pipeline describes the 3D-printing the cortical folding structure that is estimated with Freesurfer and subsequently corrected with Meshlab. And another pipeline describes how you can 3D-print any binary nii-volume by using the AFNI-program IsoSurface and correct the output with netfabb. Continue reading “3D-printing nii data”
How to convert any paper figure into a layer-profile
Often we would like to normalize depth-dependent fMRI signals and assign it to specific cytoarchitectonially defined cortical layers. However, we often only have access to cytoarchitectonial histology data in the form to figures in papers. But since we only have the web-view or the PDF available, we cannot easily extract those data as a layer-profile. Since most layering tools are designed for nii data only, paper figures (e.g. jpg or GNP) are not straight-forwardly transformed to layer profiles.
In this blob post, I describe a set of steps on how to convert any paper figure into a nii-file that allows the extraction of layer profiles.
Continue reading “How to convert any paper figure into a layer-profile”
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