Neurovis: Visualizing brain signals in 3D in real-time • Hacker News Board

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

#41

Post by omginternets » Fri, Jan 05, 2018, 5:22 PM UTC

GistNoesis wrote: post #34

omginternets wrote: post #30

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…

>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-oxygenated hemoglobin rather than a net direction of blood movement. This is sometimes confused with "blood flow", and I've been guilty of interchanging the two terms myself :/ I suspect the fluid dynamics of blood in the head is outrageously noisy and difficult to contrast out or filter though statistical means (because it's roughly random).

Concerning the relationship between neural activity and BOLD signal this paper [https://www.nature.com/articles/35084005] is a good starting point. I'll see if I can dig up the PDF for you.

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

#42

Post by neuromantik8086 » Fri, Jan 05, 2018, 5:28 PM UTC

frereubu wrote: post #18

xab9 wrote: post #14

Earlier quoted context omitted.

I had multiple MR and CT scans, some EEG - from all these only EEG is kinda "realtimish", isn't it? Do we have any technology in these days that can _map_ surface electrical changes to brain internals (depth data) or anything that can work in true 3d?

Yep, only EEG gives you that kind of information. fMRI takes a lot of post-processing with complex statistics to produce any kind of useful information. I worked on a study that used fMRI to study the involvement of early visual areas in the cortex during reading tasks, and when processing long runs we'd get on with other stuff while the data was being processed. There isn't any existing tech to take surface data and…

> 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...

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

#43

Post by neuromantik8086 » Fri, Jan 05, 2018, 5:30 PM UTC

yorwba wrote: post #10

arca_vorago wrote: post #9

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…

And part of the reason EEGs have poor sensor density is that attaching and removing them is a pain in the ass, especially if you have long hair. I participated in a study where my EEG was taken while I watched some random videos, and half the time was spent on putting enough conductive gel in my hair below the sensors to get a stable signal, and afterwards I had to shower to get rid of the stuff. There was a bald guy…

EEG nets that use saline solutions are much more manageable than gel-based nets from what I've seen (disclaimer: only ever had to use the saline solution nets). That said, avoiding crosstalk between electrodes / bridging was a bitch.

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

#44

Post by rdruxn » Fri, Jan 05, 2018, 5:49 PM UTC

lend000 wrote: post #3

This is very cool -- does anyone have experience with the company or product? This looks like something I want for my home lab.

Cool, but practically useless.

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

#45

Post by lostlogin » Fri, Jan 05, 2018, 6:11 PM UTC

omginternets wrote: post #30

GistNoesis wrote: post #29

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…

What you want is better temporal resolution, better spacial resolution, a less restrictive environment and a more direct measure of activity. The indirect BOLD signal has a long delay and is hard to accurately separate from noise. The spatial resolution of fMRI is a fraction of that achievable by clinical imaging and the MR environment is very expensive, restrictive and generally unhelpful for many experiments.

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

#46

Post by ericjang » Fri, Jan 05, 2018, 6:11 PM UTC

omginternets wrote: post #41

GistNoesis wrote: post #34

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…

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

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

#47

Post by lostlogin » Fri, Jan 05, 2018, 6:15 PM UTC

xab9 wrote: post #14

BucketSort wrote: post #6

The consumer grade EEG's you would use for this, like Open BCI, place rudimentary sensors on the scalp. There just isn't enough information from these types of sensors to give you a real look at what signals are occurring in the brain. This is a fundamentally flawed premise and is nothing more than a toy. Real brain research must be done with FMRIs or much more accurate EEG's than consumers have access to, and instit…

I had multiple MR and CT scans, some EEG - from all these only EEG is kinda "realtimish", isn't it? Do we have any technology in these days that can _map_ surface electrical changes to brain internals (depth data) or anything that can work in true 3d?

You can do real-time fMRI for relatively simple tasks. Saying a word, tapping a finger, moving the tongue. “Real-time” is the wrong phrasing as the data builds up over several runs but you see it as it builds and get something useful a minute of two into acquisition.

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

#48

Post by Batman10232 » Fri, Jan 05, 2018, 6:29 PM UTC

neuromantik8086 wrote: post #42

frereubu wrote: post #18

Earlier quoted context omitted.

Yep, only EEG gives you that kind of information. fMRI takes a lot of post-processing with complex statistics to produce any kind of useful information. I worked on a study that used fMRI to study the involvement of early visual areas in the cortex during reading tasks, and when processing long runs we'd get on with other stuff while the data was being processed. There isn't any existing tech to take surface data and…

> 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 BROCCOLI, or PSOM haven't taken off.

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

#49

Post by Batman10232 » Fri, Jan 05, 2018, 6:44 PM UTC

frereubu wrote: post #18

xab9 wrote: post #14

Earlier quoted context omitted.

I had multiple MR and CT scans, some EEG - from all these only EEG is kinda "realtimish", isn't it? Do we have any technology in these days that can _map_ surface electrical changes to brain internals (depth data) or anything that can work in true 3d?

Yep, only EEG gives you that kind of information. fMRI takes a lot of post-processing with complex statistics to produce any kind of useful information. I worked on a study that used fMRI to study the involvement of early visual areas in the cortex during reading tasks, and when processing long runs we'd get on with other stuff while the data was being processed. There isn't any existing tech to take surface data and…

EEG can do real time imaging because the sampling rate is much better. EEG also requires fairly intensive data processing, but usually it can be done faster than fMRI because: 1. There is often less/different information in EEG. If you have 64 nodes, you will have less information to process than the >100000 voxels in fMRI. 2. There have been more reasons to look at EEG in real time. fMRI analyses are generally done with group level statistics, so usually you have to run many participants which takes weeks-months anyways.

>There isn't any existing tech to take surface data and "map" it to internal states

Eh, sort of. Algorithms like LORETA which do source reconstruction have been around for a while, and do an OK job of finding the general area of the source of a signal.

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

#50

Post by GistNoesis » Fri, Jan 05, 2018, 6:45 PM UTC

ericjang wrote: post #46

omginternets wrote: post #41

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, 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).