Hi Raf, Right now users can upload, analyse and share their data and analysis with others. We didn't put the option to 'fetch' pubic data as a feature. But let me know if you are interested in that ;)
Neurosurgery is a 'champion' user of Diffusion MRI and tractography. White matters tracts are a tangible usage of the 3d maps, since it allows for presurgical planning of tumor ressection for instance, and also integrate surgical navigation systems with these maps, to GPS guide the surgery. I think the interesting challenge in what you describe is the combination of the 2 points: 1. imaging (MRI, microscopy, etc) to get quantified and quantifiable features about the tissue 2. CNNs and nupic to predict the growth growth, where it will attack next to give the 'coordinates' of where and how to treat it to prevent nasty consequences. I wonder if the 'time resolution' of the data. How nupic handles 'low frequency' time points? Cheers, Paulo On Mon, Jan 18, 2016 at 7:32 PM, Raf <[email protected]> wrote: > Hi Paulo! > > Thanks a lot for the link (www.mint-labs.com). I didn't know about your > company but it looks like you're running a really wicked project! I'd love > to test the beta for the 3d visualization. > I registered to mint-labs but I couldn't see how I can download your data > (I'm also interesting in machine learning myself) - is there maybe some > link I didn't check? > > I also noticed that you apply your mlearning techniques to other > neurologically interesting exams, such as EEG, MEG and PET: that's > fantastic. > > I'm aware that in the ward where I'm doing my internship as an undergrad > surgeons tend to use a C-Arm (something like this > http://usa.healthcare.siemens.com/clinical-specialities/surgery/surgical-disciplines/neurosurgery) > for both spinal and brain surgery: for example in the case of some > aggressive brain tumor, such as a blastoma, a common combo would be C-Arm + > Surgical Navigation System (something like this > http://www.medtronic.com/for-healthcare-professionals/products-therapies/neurological/surgical-navigation-and-imaging/neurosurgery-imaging-and-surgical-navigation/ > , which essentially is a supercool GPS where the Earth is the brain and the > hand of the surgeon are like satellites) + 5-aminolevulinic acid (for > fluorescence guide surgery) + microscope (of course). > > Unfortunately, pretty often, the 5-ala is not able to impregnate well > enough the totality of the cancerous cells, which of course means that the > surgeon can't distinguish them from the healthy tissue and, > consequentially, not being able to remove them all, their presence could > result in a tumoral relapse. > Considering that both the microscope (live) and the C-Arm (whenever the > surgeons uses it) return an imagine with potentially a decent resolution, > do you think it would be mad to try to attempt to see how some > convolutional neural network would perform against 5-ala in detecting > healthy and cancerous tissue? > > My idea would be this: > > - CNNs/RNNs --> to analyze the bare "screenshot" (or frames) coming from > the microscope and the C-Arm; > > - NuPIC "GPS" System --> to be adapted for the coordinates given by the > Surgical Navigation System and trying to predict where potentially the > tumors "goes" (certain tumors have really nasty shapes and there are really > tiny little cellular lines that squeeze into distant part of the brain - > same thing goes for certain spinal tumors). > > Would this seem possible to do? > > I'm sorry if I had to give these kind of basic explanations but I did it > in order to keep the topic interesting and relevant for other people who > may read this email that maybe are not familiar with the topic :) > > Thanks, > Raf > > > > On 15/01/2016 20:42, Paulo Rodrigues wrote: > > Hi. > > Yes, MRI (and especially brain MRI) provides 'static' images - either > showing the structure as gray matter or white matter (like from diffusion > MRI) or other modalities. > But if you want a time series on it I would say fMRI is more interesting, > as it measures 'brain activity' as a proxy from the blood oxygenations, > i.e. if part of the brain is working more, it is consuming more energy, so > it needs more blood. fMRI is discussable, or better the conclusion that are > drawn from it, especially in the task based studies. > > Now what is particularly of interest and cool is resting state fMRI > <https://en.wikipedia.org/wiki/Resting_state_fMRI> - the subject is not > doing any task, simply resting in the scanner, and the brain is > 'fluctuating' in it's "idle mode". And then you can do cool stuff like look > at the brain as a network, and as a dynamic network. This is being actively > researched as a predictor for pathologies, cognition, etc etc - and it also > has some nice connections with philosophy :) It has difficulties in the > possibilities of analysis methods and pre-processing it, but depending on > your brother's research needs, something can be done more or less complex. > > We have bunch of data if you need. Just let me know. > > Have a great weekend! > Paulo > > ᐧ > > On Fri, Jan 15, 2016 at 8:26 PM, Matthew Taylor <[email protected]> wrote: > >> Mark, Marion, or Kentaro might have something to say abou this. Also, >> here are some examples of similar projects: >> >> - >> https://www.youtube.com/watch?v=gzfTZhd6X9c&index=12&list=PL3yXMgtrZmDqZc2m7qI3Kkbmxechp2-Zs >> - >> https://www.youtube.com/watch?v=Ij4StdJBxEo&index=17&list=PL3yXMgtrZmDqZc2m7qI3Kkbmxechp2-Zs >> >> >> --------- >> Matt Taylor >> OS Community Flag-Bearer >> Numenta >> >> On Thu, Jan 14, 2016 at 1:09 PM, gideon isaac <[email protected]> >> wrote: >> >>> I was looking at some of the audio applications of Nupic provided by a >>> helpful person on this list, and I think the same methods could be used for >>> an MRI application. >>> Static MRI pictures are constructed from Fourier transforms of a signal >>> produced by Hydrogen atoms spinning under the influence of MRI magnets. >>> They are then converted into a picture. So temporal is converted to >>> spatial or vice versa. I’m somewhat muddled on this, but my brother >>> creates sequences for MRI machines and then gathers the data coming out, >>> and I want to interest him in Nupic. >>> MRI static pictures are usually used to look for anomalies like tumors, >>> or soft tissue problems that do not show up on x-rays. It might be hard to >>> compare a pathology picture with a healthy picture because people vary in >>> height and shape etc. That could be a problem – there is no standard >>> picture of a lung for instance – you would have to feed pictures from >>> people of all sizes into the HTM. >>> There would be no need for a step of converting the signal to a picture, >>> instead the signal would be fed directly into Nupic. >>> There is also Functional-MRI – which can watch movements – you can watch >>> a MRI movie of a heart beating and look for anomalies there. >>> So is this something I can present to my brother’s research team at his >>> university, and if so, are there any special methods that should be used? >>> Thanks. >>> >> >> > > > -- > > > *Paulo Rodrigues, PhD CEO & co-founder * > > > > *Arc de Sant Silvestre 4, entresuelo segunda 08003 Barcelona, Spain Tel. > +34 933 282 007 <%2B34%20933%20282%20007> Mob. +34 633 817 514 > <%2B34%20633%20817%20514> *[email protected] > www.mint-labs.com > > > -- > Raf > www.madraf.com/algotrading > reply to: [email protected] > skype: algotrading_madraf > > -- *Paulo Rodrigues, PhDCEO & co-founder* *Arc de Sant Silvestre 4, entresuelo segunda08003 Barcelona, SpainTel. +34 933 282 007Mob. +34 633 817 514*[email protected] www.mint-labs.com
