- Видео 47
- Просмотров 11 377
ofgulban
Добавлен 9 ноя 2011
I am a magnetic resonance imaging (MRI) researcher specialized in very high resolution imaging of living humans using ultra high field MRI (at 7 Tesla). In this channel, I am sharing my scientific work, showing the programs I use and documenting the tools I am developing.
Let's Analyze E004 - Simple segmentation on 0.1 mm human brain MRI
In this video, I am showing to my collaborator Alard Roebroeck (www.cbclab.org/) how I have analyzed small regions of interest on his excellent high resolution human brain MRI data (at 0.1 mm isotropic resolution, post mortem human brain).
The main point of this video is to show a dependable fall-back option for acquiring high accuracy and precision and throughly quality controlled cortical gray matter segmentations. We use such segmentation then for further cortical layer analyses.
Previous Let's Analyze video that includes segmentation is here: ruclips.net/video/tIuKG3rtVk4/видео.html
Software used in this video are:
- ITKSNAP 4.2.2: www.itksnap.org/pmwiki/pmwiki.php
- LayNii 2.7.0: github.c...
The main point of this video is to show a dependable fall-back option for acquiring high accuracy and precision and throughly quality controlled cortical gray matter segmentations. We use such segmentation then for further cortical layer analyses.
Previous Let's Analyze video that includes segmentation is here: ruclips.net/video/tIuKG3rtVk4/видео.html
Software used in this video are:
- ITKSNAP 4.2.2: www.itksnap.org/pmwiki/pmwiki.php
- LayNii 2.7.0: github.c...
Просмотров: 44
Видео
Let's Analyze E003 - Registration for infant subcortex probabilistic maps
Просмотров 9121 день назад
Here I am showing how to make probabilistic maps from manually segmented infant subcortical regions. I am using affine transformations to register 10 infant brains to a template and then show how to compute the probabilistic maps. This is a response to the conversations I have had in a meeting with Siham Ijjou Kadiri from the University of Barcelona. Software: - Python scripts are here: github....
BrainVoyager Tips and Tricks - Transparent Thresholding
Просмотров 2621 день назад
Here I am showing an alternative statistics visualization mode in BrainVoyager that adjust the transparency of statistical values based on their significance. See further details of the BrainVoyager software at: www.brainvoyager.com/ Data used in this video is acquire from: www.newbi4fmri.com/tutorial-1-data
Tutorial - Register anatomical to functional data for partial brain coverage
Просмотров 1393 месяца назад
In this video I am showing how to quickly register a whole brain T1 weighted MRI data onto the partial brain coverage functional MRI data using regions of interests to drive the automatic registration. # Used software - ITKSNAP v4.0.0: www.itksnap.org/pmwiki/pmwiki.php
OHBM 2024 Brainhack Results Presentation: Understanding fMRI
Просмотров 1153 месяца назад
Github page: github.com/ofgulban/understanding_fMRI Brainhack project page: github.com/ohbm/hackathon2024/issues/17 # Participants Omer Faruk Gulban (Project Lead) Ana Arsenovic Marshall Xu Quentin Dessain Aram Salehi Sophie Raible Kenshu Koiso Junting Peng
ISMRM 2024 Talk (1070) - Phase Jolt MRI
Просмотров 1459 месяцев назад
Title: Phase jolt: Second spatial derivative of phase images is a new contrast that offers many benefits for SWI type processing Authors: [1, 2] Ömer Faruk Gülban, [3] Andreas Deistung, [4] Desmond Ho Yan Tse, [5] Saskia Bollmann, [6] Renzo Huber, [1, 2] Rainer Goebel, [7] Kendrick Kay, [1] Dimo Ivanov [1] Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht ...
ISMRM 2024 Talk (0959) - Multi-slab whole-brain in vivo 0.35 mm human brain at 7 T
Просмотров 1779 месяцев назад
Title: Multi-slab whole-brain in vivo 0.35 mm human brain at 7 T with low undersampling to validate future acceleration & denoising Authors: [1, 2] Omer Faruk Gulban, [3] Logan T. Dowdle, [4] Desmond Ho Yan Tse, [5] Saskia Bollmann, [1, 2] Rainer Goebel, [1] Benedikt A. Poser, [1] Dimo Ivanov [1] Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University...
Treeshrew cortical layers as triangular meshes
Просмотров 93Год назад
In this video, I show how to generate cortical layer triangular meshes for treeshrew brains. I used: - ITKSNAP for editing segmentations: www.itksnap.org/pmwiki/pmwiki.php - LayNii LN2_RIMIFY and LN2_RIM_POLISH to smooth out the manual editing artifacts: github.com/layerfMRI/LayNii - bvbabel to convert nifti files into BrainVoyager file formats: github.com/ofgulban/bvbabel/tree/main/misc/video-...
OHBM Brainhack 2023 - k particles: experiments in k space
Просмотров 185Год назад
OHBM Brainhack 2023 "k particles" project results. Contributors are: - Alessandra Pizzuti - Kenshu Koiso - Paul Taylor - Thomas Maullin - Kevin R. Sitek - Fernanda Ponce - Jeff Mentch - Omer Faruk Gulban
Tutorial - Plot Layer Profiles
Просмотров 120Год назад
In this video, I am showing how to plot cortical gray matter "layer profiles" with python scripting using matplotlib. # Used software - ITKSNAP 4.0.0: www.itksnap.org/pmwiki/pmwiki.php - niimath: github.com/rordenlab/niimath - Python 3.10.9: www.python.org/ - matplotlib 3.7.1: matplotlib.org/ - LayNii 2.4.0: github.com/layerfMRI/LAYNII - LayNii_Extras: github.com/ofgulban/LAYNII_extras
Tutorial - Reslice nifti files to the same dimension and resolution
Просмотров 291Год назад
In this video, I am showing how to reslice different nifti files into a reference files data dimensions and resolution using ITKSNAP's registration feature to answer a question asked in LayNii issues: github.com/layerfMRI/LAYNII/issues/78 # Used software - niimath: github.com/rordenlab/niimath - ITKSNAP 4.0.0: www.itksnap.org/pmwiki/pmwiki.php
Tutorial - Align human subcortex to MNI space using ITKSNAP and BrainVoyager
Просмотров 264Год назад
In this video I am showing how to quickly align an individual's T1 weighted whole brain MRI data to MNI space. I am only considering the subcortical regions and not the cortex. At the end, I am also showing how to load the aligned files within BrainVoyager. # Used software - Niimath: github.com/rordenlab/niimath - ITKSNAP v4.0.0: www.itksnap.org/pmwiki/pmwiki.php - BrainVoyager v22.4.4: www.bra...
Let's Analyze E002 - LayNii layers and flattening fMRI activity in V1
Просмотров 249Год назад
In this video, I am showing how to get cortical layers and flatten a portion of V1 to investigate fMRI activity patterns.
Practical LayNii - Flattening cortex in 2D histology images
Просмотров 175Год назад
Here, I am showing how to flatten the visual cortex using LayNii. Data provided by Michael Arcaro: www.arcarolab.org/ - LayNii v2.4.0: github.com/layerfMRI/LayNii - niimath v1.0.20220720: github.com/rordenlab/niimath - ITKSNAP v 4.0.0: www.itksnap.org/pmwiki/pmwiki.php
Let's Analyze E001 - High res VASO fMRI cortical segmentation, LayNii layers and more
Просмотров 541Год назад
Here I am challenging myself by segmenting a dataset that I see for the first time. This dataset is a submillimeter VASO fMRI dataset. And the rule is simple: I can only use a single 3D image. Can I do it in my first try, or not? Let's find out. This is a response to the conversations I have had in a lab meeting ruclips.net/video/0zAdp0xPh4w/видео.html - ITKSNAP 4.0.0 www.itksnap.org/pmwiki/pmw...
Tutorial - Phase image cyclic color maps in ITKSNAP
Просмотров 159Год назад
Tutorial - Phase image cyclic color maps in ITKSNAP
Tutorial - Inverse grayscale in ITKSNAP
Просмотров 475Год назад
Tutorial - Inverse grayscale in ITKSNAP
Tutorial - Intro to segmentation in ITKSNAP
Просмотров 3,7 тыс.Год назад
Tutorial - Intro to segmentation in ITKSNAP
Human Connectome Project (HCP) atlas resampled on high density surfaces.
Просмотров 256Год назад
Human Connectome Project (HCP) atlas resampled on high density surfaces.
BrainVoyager Tips and Tricks - Segmentation of MP2RAGE 7 T MRI data
Просмотров 404Год назад
BrainVoyager Tips and Tricks - Segmentation of MP2RAGE 7 T MRI data
CMRR Seminar Talk - Mesoscopic Cortical Landscape at 0.35 mm Isotropic Resolution
Просмотров 942 года назад
CMRR Seminar Talk - Mesoscopic Cortical Landscape at 0.35 mm Isotropic Resolution
OHBM Brainhack 2021 - Flooding Brains Project Results
Просмотров 442 года назад
OHBM Brainhack 2021 - Flooding Brains Project Results
OHBM Brainhack 2022 - Exploding Brains Project
Просмотров 1482 года назад
OHBM Brainhack 2022 - Exploding Brains Project
OHBM 2022 - Poster WTh534 - Cake plots
Просмотров 842 года назад
OHBM 2022 - Poster WTh534 - Cake plots
ISMRM 2022 - Power Pitch (0687) at 1080p - Brain in a virtual Petri dish
Просмотров 3242 года назад
ISMRM 2022 - Power Pitch (0687) at 1080p - Brain in a virtual Petri dish
LayNii Tutorials - 010 - LN2_PATCH_FLATTEN - How many bins?
Просмотров 872 года назад
LayNii Tutorials - 010 - LN2_PATCH_FLATTEN - How many bins?
LayNii Tutorials - 009 - LN2_PATCH_FLATTEN - Inputs and Outputs
Просмотров 1122 года назад
LayNii Tutorials - 009 - LN2_PATCH_FLATTEN - Inputs and Outputs
LayNii Tutorials - 008 - LN2_MULTILATERATE - Norms and Angles
Просмотров 592 года назад
LayNii Tutorials - 008 - LN2_MULTILATERATE - Norms and Angles
LayNii Tutorials - 007 - LN2_MULTILATERATE - Custom Axes
Просмотров 742 года назад
LayNii Tutorials - 007 - LN2_MULTILATERATE - Custom Axes
LayNii Tutorials - 006 - LN2_MULTILATERATE - Road to Flat Brains
Просмотров 1552 года назад
LayNii Tutorials - 006 - LN2_MULTILATERATE - Road to Flat Brains
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Thanks Faruk. What would be the additional steps to get the ultimate registration? Do you use any tools to quantify the registration between multiple functional data sets?
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How do i load several segmentation images onto one and make them both visible at the same time?
33597 Antonio Ports
Very impressive work!
I thought it was a horror video
Why not jst select the 3D option for the brush?
Because 3D brush edits slices that you are not seeing, which causes boundary errors when segmenting highly curved structures.
thankyou
Thank you. I was wondering: After segmenting a ROI, how can I save it in a binary format?
You can Go to segmentation tab and save the segmentation. This will create a binary file if you used only label 1 (single color).
Eline sağlık güzel video.
Hello, how to calculate segment of grey and white matter in itch hemispheres? (Volume of greys and white matters) Thanks
uhm, there are many ways. Maybe too many to list here. But you can have a look at FSL-FAST, freesurfer, BrainVoyager Advanced Segmentation, SPM programs to begin with. Maybe have a look at : Helms, G., 2016. Segmentation of human brain using structural MRI. Magnetic Resonance Materials in Physics, Biology and Medicine 29, 111-124. doi.org/10.1007/s10334-015-0518-z paper as well
k-space cellular automata rocks! Whose face it was though 5:24? :D
The face belongs to one of our team members, Kevin. Who had the initial idea to use a face as a kernel in k space.
Promo>SM
3:42 is Game of Life? 🤔😂
indeed 👾👾👾
Hello, thanks very much for your videos. Can you release the code about transforming freesurfer aseg file to laynii rim file?
Hi, somehow the link in the description got broken. Here is the new link: github.com/ofgulban/LAYNII_extras/blob/38e607edbd6601b5893e519af3f791059fbe190d/demo-freesurfer_segmentation_to_rim/freesurfer_segmentation_to_rim.py
Also, we are going to add direct conversion option into LN2_RIMIFY in the near future (that will not require the extra python script). You can see the progress at: github.com/layerfMRI/LAYNII/issues/74
Wow ! Just wow! Great job.
Thanks Sean :)
Awesome work guys!
Wow so hypnotizing! Amazing work Faruk!
you have my vote
Thank you for the very clear explanation on how to implement it and what motivation behind is. Really useful!
Brains
Love it
Great work! Can't wait to try it out.
Great talk Faruk