
MRI Scans of a person's brain - shagunsodhani
https://github.com/dcunited001/mri-scans
======
trickyager
Just as a general note, these images contain personally identifying
information about the patient. This includes not just the patient's name, but
also his age, address, phone number, and an extremely limited health history.

~~~
dcunit3d
For the record, i wanted to post my brain online for many reasons. First of
all, I did it for science of course. It'd be great for more of this data to be
available online for people to study and work with.

There are many anonymized datasets available on Radiopaedia.
[http://radiopaedia.org/](http://radiopaedia.org/) I've spent quite a bit of
time studying neurological conditions on that site and on wikipedia. Those are
more useful, but anonymized. I'm not sure that there are many healthy MRI
datasets available there, which makes it more difficult to statistically model
MRI data.

I'm hoping to use Nipy and Dipy to create visualizations of my brain. In
particular, i'm hoping to recreate some of the Diffusion Tensor Imaging work
in this talk by Ariel Rokem:
[https://www.youtube.com/watch?v=HdrSZtB0uX0](https://www.youtube.com/watch?v=HdrSZtB0uX0).
However, i'm not sure if my DT images are high enough resolution.

I also did it for philosophical reasons. I believe that all digitized
information past and present will be inevitably become known & public post
facto. It's the nature of information & knowledge in our technological world
to distribute itself until the world converges on total information
omnipresence. So if, in the end, all [digitized] information is known, then
there is no point in hiding information. This is more of a philosophical
viewpoint though. obviously it's impossible for all information to converge in
this way.

But this is true even of our own minds. And if our mind can be digitized from
our brain, this also has interesting security implications. If you've seen the
show stitchers, then you know what i mean.

Under no circumstances was this done in the name of art.

~~~
marmaduke
Thanks for posting your scans. As noted in the issue I just made (I am @maedoc
on Github), if you add the diffusion imaging scans we can virtualize your
brain [1] and simulate it [2].

What strength MRI was used for the scans? 1.5T, 3T, 7T?

[1] github.com/timpx/scripts [2] github.com/the-virtual-brain/tvb-library

~~~
david-given
I doubt the scans really high enough resolution for a meaningful simulation
--- I don't believe MRI scans can capture the complete connectome of a single
human brain, let alone any subcellular data.

e.g. the Human Connectome Project is still working on capturing the macroscale
connectome, that is, high level structures only. Recording the microscale
connectome, that is, the neuronal structure, currently requires destroying the
brain you're analysing.

~~~
shpx
You need at least 10 picometer percision to go down to the cell level (1.5L /
86 billion neurons), MRIs are 1mm according to the talk dcunit3d posted [0].

[0]
[https://www.youtube.com/watch?v=HdrSZtB0uX0](https://www.youtube.com/watch?v=HdrSZtB0uX0)

~~~
amluto
10 picoliter, perhaps? That's much less crazy than 10 picometer.

But you want the dendrites, too, not just cells.

------
rogeryu
Last year an MRI scan was made of my brain. This was part of a promotion
research at the university. All I got back was a lousy screenshot of my brain.
;-)

No but seriously - it was a big shock to see my brain in a picture. It is a
really weird experience, similar when I saw myself for the first time on film.
Maybe this is a normal experience for the current generation, but I hadn't
seen myself on film before age 15. You have an image how you move, what you
look like, but then you see this on film, and it's a total shocker. All these
small movements you make, typical for you, and everybody around you knows
them, except for you. So everybody else sees nothing strange when viewing that
movie, except you.

I've seen many MRI scans in films and tv series, although I can't remember one
since then. From these I have a general picture of what a brain looks like.
I've seen plastic 3D brain models. And then I see my brain and it's so
different. It's clearly me, no doubt, but still... Totally weird!!!

~~~
christiangenco
How do you feel like a low resolution 3D scan of what someone told you was the
inside of your head is clearly you? I'd feel like they could've shown me
anyone's MRI and I'd have no way of telling them apart.

~~~
rogeryu
I got one screenshot with three images in it. The (vertical) profile image is
clearly me. The other two (vertical frontal and horizontal at eye level) that
could be anyone.

~~~
christiangenco
Ahh, that's super neat. I didn't realize MRIs included vertical profiles!

------
aantix
Back in December of 2007 a nodule was detected on my lung. Not knowing what to
think of it, I posted the images on my blog and recruited other med students
to comment on the images. Here's the Way Back Machine link to the blog post.

[https://web.archive.org/web/20081205032710/http://www.runfat...](https://web.archive.org/web/20081205032710/http://www.runfatboy.net/blog/2007/12/28/diagnose-
me/)

~~~
rangibaby
So... what was it?

~~~
aantix
Ended up being benign. I probably went a bit overboard, but did a pet scan,
nothing lit up. Continued to do CT scans to monitor for growth, and it stayed
the same. I was just so scared..

------
schappim
I've submitted a pull request: [https://github.com/dcunited001/mri-
scans/pulls](https://github.com/dcunited001/mri-scans/pulls)

~~~
platz
you're funny

------
rdtsc
Was wondering, in the general, is the patient always the copyright owner of
this kind of data? Can they relicense it, publish it, do anything they want
with it?

It seems like that would be the case, but there has been talk about patenting
parts of the DNA in the past, and legally sometimes things work in un-expected
ways.

~~~
whybroke
You can't copyright such material at all.

[https://meta.wikimedia.org/wiki/Wikilegal/Copyright_of_X-
ray...](https://meta.wikimedia.org/wiki/Wikilegal/Copyright_of_X-ray_Images)

~~~
pak
I'm not sure how definitive that guide is. For what it's worth, all of my
medical textbooks are very careful to include licensing and attribution
information for all of their medical images, including X-rays. So even if
there's not much case law on it, publishers seem to be erring on the side of
caution.

------
anotheryou
Anything cool one can do with this? I have my MRI + DTI and wonder what to do
with it.

Mine looks like any brain to me (no tumors, yay!).

From the DTI I was able to calculate the white matter trajectory with slicer:
[http://screencast.com/t/yDYFJdL7D](http://screencast.com/t/yDYFJdL7D)

(I was a little let down I couldn't follow the visual nerves, but as they
cross there is no clear direction of diffusion that could be imaged I
guess...)

~~~
kenferry
Yes. For my girlfriend's birthday I grabbed her MRI scans, extracted the pial
surface as a mesh, 3D printed the mesh, made a silicone mold from the print,
and cast her brain in chocolate so she could eat her own brain, thus becoming
an auto-zombie.

~~~
hellofunk
I did this too, but it took much longer than the simple steps you've outlined
would seemingly take. I spent at least an hour on the whole process, which is
more than I'd prefer for something so straightforward. I blame the early tech
of 3d printing for not being as swift as I'd hoped.

~~~
devereaux
Can I email you?

~~~
hellofunk
Yes but at your own risk.

~~~
devereaux
Ok, but I would need your email :-)

I added my email to my profile.

------
meshko
Does he accept pull requests?

------
sergers
if you are interested in viewing patient scans, with the PHI anonymized but
the rest of the metadata in tact, check out:

[https://www.mypacs.net/mpv4/hss/casemanager](https://www.mypacs.net/mpv4/hss/casemanager)

(30,380 cases. 187,945 images.) its a teaching/sharing site for radiologists
where they can send the data from their PACS. this is the free public site
which includes a basic web based dicom viewer to zoom/pan/window level etc

~~~
quasarj
Or The Cancer Imaging Archive:
[http://www.cancerimagingarchive.net/](http://www.cancerimagingarchive.net/)

Though I'm not sure how much of it can be accessed without an account.

------
simonster
Here's the "Colin 27" brain atlas, derived from 27 scans of Colin J. Holmes's
brain:
[http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27](http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27)

Here's a lot of data from Russ Poldrack, who scanned his brain and collected
behavioral and metabolic data from himself very regularly over the course of a
year: [http://myconnectome.org/wp/data-
sharing/](http://myconnectome.org/wp/data-sharing/)

------
devereaux
With a usual CT scan, you can do a volume rendering. Play around with the
opacity to show the skin - this will give you a 3D image of your face.

Example on
[http://1.bp.blogspot.com/-LuLV6F-Fp0o/TbcY7BUvpjI/AAAAAAAAAM...](http://1.bp.blogspot.com/-LuLV6F-Fp0o/TbcY7BUvpjI/AAAAAAAAAMo/4AEDNzhHqko/s320/Martin%2BFace5.jpg)

With a usual MRI, unfortunately slices are too far apart to be able to stitch
them together like this.

~~~
wl
All the MRI scans of my brain I've gotten ("structural" scans taken as part of
fMRI studies) have been sufficient to get a pretty decent volume rendering of
my head. Some of them cut off about half way through the jaw, but that's
another issue entirely.

~~~
lostlogin
The research scans use 3D T1 (and sometimes T2) scans for mapping the
functional data onto a brain region. They have to put the low res functional
scans onto something that has some degree of resolution. Functional scans are
acquired with temporal resolution in mind - the change in signal after
activation is something like 6 seconds, and to accurately sample this you want
a whole brain acquisition in much less time that that. We typically acquire
whole brain scans in something like 3 seconds. New techniques such as
multiband imaging are acquiring whole brain scans in 600-700ms or so. This is
pretty fast. Clinical scans do use 3D techniques but tend to go for 2D scans
(which are a slice, then a gap of 10-30% usually of slice thickness) then a
slice. 2D scans are faster, have much better in plane resolution (lower
through plane as slices are fatter and have gaps between them). Clinical scans
are also one hell of a lot better for identifying things as numerous image
weighting a are obtained. MR tech here.

~~~
devereaux
What's the resolution of the whole brain scan you deal with in research these
day? (ie the cubic size of the voxel when acquired in 3s? What about in 600ms)

I have to keep myself up-to-date, it's been a while since I played with that!

~~~
lostlogin
I'll check - I'd guess 3mm slices but with 600ms acquisitions I haven't looked
recently enough to remember.

------
th0ma5
Can I just get an MRI or CT scan without a medical reason and at a reasonable
cost? Perhaps that is an absurd question in the United States.

~~~
neonkiwi
Find a study and sign up.

Look for research groups in your local institutions and send an email to a
couple grad students asking about studies they or their colleagues are running
in the near future. A researcher may give you the scan if you ask nicely and
say it's for personal interest, plus you'll be compensated for your time /and/
simultaneously help with the advancement science :)

------
smtpserver
I 3D printed mine (skull is from another project)
[http://i.imgur.com/BelYUSih.jpg](http://i.imgur.com/BelYUSih.jpg) and a
Blender render:
[http://i.imgur.com/oPCSxbo.png](http://i.imgur.com/oPCSxbo.png)

~~~
tdaltonc
Beautiful! What did you use to turn the DICOM/NIFTI files in to a printable
format?

------
aculver
Hey David, I didn't expect to see your brain on the front page of HN. Can you
confirm for us that everything is OK? :-)

~~~
dcunit3d
hey! yeh, everything's going well. the scans were done to help diagnose some
things about 2 years ago. nothing turned up in the scans though.

thanks for tweeting me earlier. i had no idea this was on Hacker News! lol

------
boas
Here's a normal brain MRI, compared to photographed slices of a brain:

[https://www.claripacs.com/a.php?a=vw](https://www.claripacs.com/a.php?a=vw)
(Click and drag to scroll. "Share > Download" to download the full DICOM data)

This site has thousands of anonymized MRI and CT images of normal and abnormal
scans, with clinical history in many cases. For example, here are annotated
scans of normal anatomy:

[https://www.claripacs.com/folder/Anatomy&view_type=-1](https://www.claripacs.com/folder/Anatomy&view_type=-1)

One challenge with writing web DICOM viewers is the lack of full 16 bit image
support in browsers. This requires writing custom code to properly handle
window / level on 16-bit medical images.

Disclosure: I'm a co-founder of Claripacs.

------
dmd
Wow. This goes to show that people in field X often have no idea what's
interesting to people outside their own field. My PhD is in cognitive
neuroscience, and so I have many dozens of MRIs of myself done for test or
calibration purposes, done using all sorts of different machines, sequences,
etc. It's never occurred to me that these images would be of interest to
anyone but me.

I suspect this is true for pretty much anyone in any field.

------
VeilEm
If we get better at this and are able to create detailed enough scans of a
brain maybe we can recreate that person some day, including memories and
everything.

~~~
daveguy
As kendallpark pointed out this is highly unlikely. I upvoted you because it's
an interesting "hmmm... what would it take?" The spatial resolution of an fMRI
is high compared to something like EEG, but the time resolution is much
slower. Even the spatial resolution is on the order of cubic mm at the
absolute best. So, we are no where close to being able to scan the activity of
every one of the ~100 billion neurons in a human brain and it would 7+ orders
of magnitude better spatial recognition and associated processing
capabilities. So, the magnitude of your "if" is large enough that it's on the
level of Kurzweil Crazy, but cool to think about regardless.

~~~
notgood
I know nothing about neurology, but my money would be on using a different
mechanism to extract all the data, maybe something like fake neurons that dump
all the information via WiFi, a MITM attack for the brain itself if you like.

~~~
HappyTypist
With our current understanding, such tasks are comparable to trying to break
the speed of light. However, we could probably get incredibly close without
_any_ internal data extraction. Our personalities, while highly complex, can
be approximated into some simple traits (e.g. 74% 'passive-aggressive', 47%
empathy) and replication of our knowledge isn't strictly necessary. Find
10,000 interests and create a int_8 each of how much someone is into it. Et
cetra.

------
martin1b
Anyone recommend a viewer?

~~~
McKayDavis
OsiriX [1] is a popular OS X/iOS viewer.

3DSlicer [2] is an excellent alternative that runs on Win/OS X/Linux

[1] [http://www.osirix-viewer.com](http://www.osirix-viewer.com)

[2] [http://www.slicer.org](http://www.slicer.org)

~~~
anon4711
On OS X, Horos is a free and open derivative of OsiriX.

[http://www.horosproject.org](http://www.horosproject.org)

------
Razengan
Not quiet the same, of course, but this reminds me of the game Soma, where
[SPOILERS!] the protagonist has his brain fully mapped and "uploaded" as part
of a treatment, and his scans are used as a template for A.I. research in the
future, leading him to be "reborn" a century later in a different body.

------
ciroduran
The McGill university also offers these MRI simulations, if you need brain
scans for your visualisation/processing needs.
[http://brainweb.bic.mni.mcgill.ca/brainweb/](http://brainweb.bic.mni.mcgill.ca/brainweb/)

Very useful when I did my undergraduate thesis.

------
kendallpark
This couldn't come at a more opportune time. I'm studying neuro this block and
need me some brains to look at.

~~~
piceas
I have a set of slices which weren’t so healthy. Let me know if sharing them
would be of value to you.

[https://d0921abcf0d58ba49c3d-6ecbc7565855acc8ab3c742259f09fe...](https://d0921abcf0d58ba49c3d-6ecbc7565855acc8ab3c742259f09feb.ssl.cf1.rackcdn.com/slice.jpg)

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cafebeen
For those who are interested, the human connectome project is in the process
of acquiring and publicly releasing a database of 1000+ MRIs collected from
normal subjects:

[http://www.humanconnectome.org/data/](http://www.humanconnectome.org/data/)

~~~
jpellman
For those who are interested, this Nature table summarizes the MRI datasets
that are out there:

[http://www.nature.com/neuro/journal/v17/n11/fig_tab/nn.3818_...](http://www.nature.com/neuro/journal/v17/n11/fig_tab/nn.3818_T1.html)

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amelius
This is nice. It would be even nicer if this was complemented by medical
records, and genotyping data (e.g. from 23andme).

------
akerro
I'm starting to be afraid that one day my brain, memories will be pushed on
git :<

------
zump
Now to apply compressive sensing!

