Hi Paulo!
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 ;)
Yep, that's actually what I'd like to see :)
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.
Didn't think yet of DMRI (although I love the images they create) but in
future, if it works, I will definitely try with these too!
I wonder if the 'time resolution' of the data. How nupic handles 'low
frequency' time points?
Good question (which I can't still reply to, considering I haven't tried
to fetch data from the Surgical Nav System yet).
I'll update you in future if I'm authorized to try this.
Thanks a lot for your help.
Raf
On 24/01/2016 20:16, Paulo Rodrigues wrote:
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]
<mailto:[email protected]>> wrote:
Hi Paulo!
Thanks a lot for the link (www.mint-labs.com
<http://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]
<mailto:[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] <mailto:[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 <tel:%2B34%20933%20282%20007>
Mob. +34 633 817 514 <tel:%2B34%20633%20817%20514>
/[email protected] <mailto:[email protected]>
www.mint-labs.com <http://www.mint-labs.com>
--
Raf
www.madraf.com/algotrading <http://www.madraf.com/algotrading>
reply to:[email protected] <mailto:[email protected]>
skype: algotrading_madraf
--
*Paulo Rodrigues, PhD
CEO & co-founder
*/Arc de Sant Silvestre 4, entresuelo segunda
08003 Barcelona, Spain
Tel. +34 933 282 007
Mob. +34 633 817 514
/[email protected] <mailto:[email protected]>
www.mint-labs.com <http://www.mint-labs.com>
--
Raf
www.madraf.com/algotrading
reply to: [email protected]
skype: algotrading_madraf
