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Neurovis: Visualizing brain signals in 3D in real-time

neuropro.ch

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Re: Neurovis: Visualizing brain signals in 3D in real-time

#51

Earlier quoted context omitted.

I'm not suggesting that we measure the signal emitted by the brain like EEG do. I'm suggesting that we look at the fluids movements like FMRI do but using diffraction like xray-imaging with bigger wavelengths.

>I'm suggesting that we look at the fluids movements like FMRI do but using diffraction like xray-imaging with bigger wavelengths. What would we gain from using RF-diffraction as opposed to MR? The major advantage of fMRI is that you're measuring a so-called Blood-Oxygen-Level-Dependent (BOLD) signal. That is, you're looking at a contrast between oxygenated and de-oxygenated blood, which is more interesting than just…

It’s always great to have informed responses here so thank you for contributing.

I gotta say though regarding the other comments on data quality, if a lay person read through the wiki pages on common brain imaging techniques (as I did) including fMRI, it seems easy to come away, rightly or wrongly, thinking, that’s all we have? That’s the state of the art spatial/temporal resolution? No wonder we can’t model the brain from first principles.

The amount of innovation, effort, and complexity that was needed to get imaging where it is today seems amazing to me, just glossing over the major achievements, it’s nobel prize level stuff. Yet you guys seem to have to still work in so much darkness with so little light. It seems rather than imaging one day simply revealing fundamental secrets, it’s just providing clues that will continue to require great insights and experiments to change the world.

But again, full admission of popcorn eating ignorance in these assumptions.

Re: Neurovis: Visualizing brain signals in 3D in real-time

#52
post #20

This is as useful as plotting traffic data from NY into a map of SF.

This comment could be useful if you'd explain why, but as it stands, it's just a shallow dismissal of the kind we're hoping to avoid here. Please don't post like that.

If, however, you'd like to neutrally explain the point (neutrally = without snark or spin), so we could all learn something, that would be great.

https://news.ycombinator.com/newsguidelines.html

Re: Neurovis: Visualizing brain signals in 3D in real-time

#53

Earlier quoted context omitted.

>BOLD signal is really what you want Thank you so much (I have no medical knowledge and that is some key domain-knowledge I've missed). How much correlation with blood flow is there ? Maybe the BOLD signal can be reconstructed from the graphs of all mixed blood flow. >What would we gain from using RF-diffraction as opposed to MR? Main gain is practicality. Main usage would be for brain interface. This is phase contra…

>Thank you so much My pleasure :) >This is phase contrast tomography, so you can get the refractive index of the materials inside, and their speed. This is way outside of my domain of competence, but if I understand correctly, this would not constitute a BOLD signal? I'm skeptical of the idea that blood diffusion alone correlates with cerebral activity. With fMRI, you're looking at temporary gradients of de-oxygenate…

You are right this is not a BOLD signal.

I was hoping the brain was able somehow to vaso-constrict to direct its oxygen supply toward some region and that we could observe that. But from what I'm picking from you is that it's more like there is fluid everywhere, and cells are just consuming more or less kind of an open-buffet (versus cells waiting at the table and asking for more or less food).

^^found your paper without paywall but haven't read it yet [http://wexler.free.fr/library/files/logothetis%20(2001)%20ne...]

Re: Neurovis: Visualizing brain signals in 3D in real-time

#54
post #25

Earlier quoted context omitted.

What is the most advanced open source solution to the brain computer interface issue? Afaik they had gotten pretty good at decoding even the low sensor density data into actionable input, but all solutions suffer from input/compute lag. So that said, FMRI's won't work for realtime will it due to how long scans take? So EEG's seem to be the only choice. Perhaps to make up for accuracy you have to increase sensor densi…

There are many open-source solutions for BCI projects like BCI2000 ( http://www.schalklab.org/research/bci2000 ), OpenVibe ( http://openvibe.inria.fr/ ) and EEGLab ( https://sccn.ucsd.edu/eeglab/index.php ). That's based on the kinds of tools that our customers use. Most of these, aren't as pretty as tool like Neurovis, but in reality most of the information that we make use of to control prosthetics or signal intent…

Thank you so much for taking the time to answer my questions. Looks like I have some reading up to do.

The reason I ask about this is because my long term thinking is that while motion controlled virtual reality is fun and going to be good for exercise games and training, I think human-brain-computer interface represents the most promising of the interaction methods (nothing says you can't be hooked up and still typing, using a mouse, or motioncontrolling either).

You mentioned the medical desire of seeing deeper brain waves, but I just want to control a computer, so given the current state of the EEG's are they useful yet as a practical operating system control input?

Re: Neurovis: Visualizing brain signals in 3D in real-time

#55

Earlier quoted context omitted.

> when processing long runs we'd get on with other stuff while the data was being processed. The main reason why fMRI processing takes so long is the reluctance of the major neuroimaging suites to embrace GPUs. A newer suite, BROCCOLI [1], is substantially faster but has much less adoption and isn't quite as full-featured as the other suites. [1] https://www.frontiersin.org/articles/10.3389/fninf.2014.0002...

Not just GPUs, most labs don't embrace parallelism in general. I managed to get a 55x speedup between serial and parallel versions using the same program (SPM) by using several mid-grade computers and caching (Sorry I don't have anything written on this, I've been putting it off). It's hard to get researchers to switch using the algorithms that they know and are comfortable with, which is why I think stuff like BROCC…

[deleted]

Re: Neurovis: Visualizing brain signals in 3D in real-time

#56

Earlier quoted context omitted.

>Thank you so much My pleasure :) >This is phase contrast tomography, so you can get the refractive index of the materials inside, and their speed. This is way outside of my domain of competence, but if I understand correctly, this would not constitute a BOLD signal? I'm skeptical of the idea that blood diffusion alone correlates with cerebral activity. With fMRI, you're looking at temporary gradients of de-oxygenate…

You are right this is not a BOLD signal. I was hoping the brain was able somehow to vaso-constrict to direct its oxygen supply toward some region and that we could observe that. But from what I'm picking from you is that it's more like there is fluid everywhere, and cells are just consuming more or less kind of an open-buffet (versus cells waiting at the table and asking for more or less food). ^^found your paper wit…

>wexler.free.fr

Holy shit, I am laughing my ass off. That domain belongs to a guy in my former lab :'D

Re: Neurovis: Visualizing brain signals in 3D in real-time

#57

Earlier quoted context omitted.

>I'm suggesting that we look at the fluids movements like FMRI do but using diffraction like xray-imaging with bigger wavelengths. What would we gain from using RF-diffraction as opposed to MR? The major advantage of fMRI is that you're measuring a so-called Blood-Oxygen-Level-Dependent (BOLD) signal. That is, you're looking at a contrast between oxygenated and de-oxygenated blood, which is more interesting than just…

It’s always great to have informed responses here so thank you for contributing. I gotta say though regarding the other comments on data quality, if a lay person read through the wiki pages on common brain imaging techniques (as I did) including fMRI, it seems easy to come away, rightly or wrongly, thinking, that’s all we have? That’s the state of the art spatial/temporal resolution? No wonder we can’t model the brai…

You hit the nail on the head. Cognitive neuroscience -- especially WRT functional imagery -- reminds of the fable of the blind men and the Elephant.

(Very) roughly speaking, you have the choice between:

- Excellent temporal resolution & crappy spatial resolution (EEG / MEG)

- Pretty good spatial resolution & crappy temporal resolution (fMRI)

Other techniques (NIRS, TMS, etc) fall somewhere along the spectrum and have their own quirks. We're peering into brain function with a super-low-res "camera" and attempting to draw only the roughest contours of the thing we're exploring.

Re: Neurovis: Visualizing brain signals in 3D in real-time

#58

Earlier quoted context omitted.

>Thank you so much My pleasure :) >This is phase contrast tomography, so you can get the refractive index of the materials inside, and their speed. This is way outside of my domain of competence, but if I understand correctly, this would not constitute a BOLD signal? I'm skeptical of the idea that blood diffusion alone correlates with cerebral activity. With fMRI, you're looking at temporary gradients of de-oxygenate…

Does de-oxygenated blood have a measurably different refractive index w.r.t. radio waves than oxygenated blood?

No, but de-oxygenated hemoglobin is paramagnetic, and therefore detectable using what's called T2*-weignted scan sequences.

http://casemed.case.edu/clerkships/neurology/Web%20Neurorad/...

Re: Neurovis: Visualizing brain signals in 3D in real-time

#59

Earlier quoted context omitted.

Does de-oxygenated blood have a measurably different refractive index w.r.t. radio waves than oxygenated blood?

No, that's why MRI has an undeniable advantage if it's what's important. What I was hoping, was that if the brain is somehow "opening" the various valves to bring more juice to certain area then that would be useful info (regardless of whether or not there is O2 in the blood, and where this O2 is consumed).

I see, so you are proposing a way to infer capillary expansion/contraction as a way to measure blood flow.
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