[Sidefx-houdini-list] MRI Data / level set grids

Michael Montoya montoyland at gmail.com
Thu Aug 11 09:21:12 EDT 2011


A couple of years back I found myself working on a similar project and the best piece of software I was able to find was VolView. http://www.kitware.com/products/volview.html 
It will read DICOM data and allow you to dial-down through the color thresholds to hone in on the tissues you are interested. Not only will it output a movie of your visualization - but it will also generate a point cloud of your geometry that you can clean up in   most modeling packages. 

If you're looking for raw DICOM data, the best source is the Visible Human Project. They offer highly detailed slices (the cadavers were literally frozen inside a block, sliced at regular intervals and then photographed with color film). The fidelity is hard to beat even with MRI. You can gain access to the data with a reasonable project proposal - you should have no issues if  it's for public use. http://www.nlm.nih.gov/research/visible/visible_human.html

Interested to see what you do with this - post back with results when you're done!
Best of luck,
Mike

On Aug 11, 2011, at 8:48 AM, sidefx-houdini-list-request at sidefx.com wrote:

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> Today's Topics:
> 
>   1. MRI data / level set grids request (Martin Sawtell)
>   2. Re: MRI data / level set grids request (Stephen Tucker)
>   3. Re: MRI data / level set grids request (Martin Sawtell)
>   4. Re: MRI data / level set grids request (Martin Sawtell)
>   5. Re: MacBook Pro compatibility (Ron Schab)
>   6. Re: MacBook Pro compatibility (Mark Alexander)
>   7. Re: Geometry ROP HDA (Magnus Pettersson)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 11 Aug 2011 10:04:19 +1000
> From: Martin Sawtell <martin at msawtell.com>
> Subject: [Sidefx-houdini-list] MRI data / level set grids request
> To: sidefx-houdini-list at sidefx.com
> Message-ID:
>    <CABrzp6x2zOugJT91KmJcA-8yPUBgxQHqD+OAeb78D6O8_=o82A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hey all, I have a bit of an odd request; I'm hunting around for ideally a
> scan of a brain which I can convert into an SDF or combination of volumes in
> Houdini. I've actually got some DICOM slices of my own head but the spacing
> is >2cm so there aren't really enough to extract a nice volume from it. Then
> there is the whole issue of processing the DICOMs to get a nice
> representation of densities and different tissue types.
> 
> So if offhand anyone knows where to find something (any body
> part/animal/cool thing) which I could wrangle a houdini volume from please
> let me know. This is for a personal project, not production and will be made
> publicly available when I've got it working... It will be a bit of a
> surprise what I'm doing with it :D
> 
> cheers
> M
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 11 Aug 2011 10:07:19 +1000
> From: Stephen Tucker <stucker at allegrodigital.com>
> Subject: Re: [Sidefx-houdini-list] MRI data / level set grids request
> To: <sidefx-houdini-list at sidefx.com>
> Message-ID: <BAY145-W5838F590316026FAE7919F9E220 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> Not MRI, but potentially useful if you took the frames
> 
> http://fstoppers.com/light-painting-with-1871-slices-of-a-corpse
> 
> 
>> Date: Thu, 11 Aug 2011 10:04:19 +1000
>> From: martin at msawtell.com
>> To: sidefx-houdini-list at sidefx.com
>> Subject: [Sidefx-houdini-list] MRI data / level set grids request
>> 
>> Hey all, I have a bit of an odd request; I'm hunting around for ideally a
>> scan of a brain which I can convert into an SDF or combination of volumes in
>> Houdini. I've actually got some DICOM slices of my own head but the spacing
>> is >2cm so there aren't really enough to extract a nice volume from it. Then
>> there is the whole issue of processing the DICOMs to get a nice
>> representation of densities and different tissue types.
>> 
>> So if offhand anyone knows where to find something (any body
>> part/animal/cool thing) which I could wrangle a houdini volume from please
>> let me know. This is for a personal project, not production and will be made
>> publicly available when I've got it working... It will be a bit of a
>> surprise what I'm doing with it :D
>> 
>> cheers
>> M
>> _______________________________________________
>> Sidefx-houdini-list mailing list
>> Sidefx-houdini-list at sidefx.com
>> https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list
>                         
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 11 Aug 2011 10:14:27 +1000
> From: Martin Sawtell <martin at msawtell.com>
> Subject: Re: [Sidefx-houdini-list] MRI data / level set grids request
> To: sidefx-houdini-list at sidefx.com
> Message-ID:
>    <CABrzp6xZfg+gkhLkusoWUdZua9DdeV8ebqXxSnL7DCnU4SxcyQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Yes! Anything with lots of slices and some nice contrasts in colours/values
> to make it easier to segment up/filter. Good stuff.
> 
> -M
> 
> 
> On 11 August 2011 10:07, Stephen Tucker <stucker at allegrodigital.com> wrote:
> 
>> 
>> Not MRI, but potentially useful if you took the frames
>> 
>> http://fstoppers.com/light-painting-with-1871-slices-of-a-corpse
>> 
>> 
>>> Date: Thu, 11 Aug 2011 10:04:19 +1000
>>> From: martin at msawtell.com
>>> To: sidefx-houdini-list at sidefx.com
>>> Subject: [Sidefx-houdini-list] MRI data / level set grids request
>>> 
>>> Hey all, I have a bit of an odd request; I'm hunting around for ideally a
>>> scan of a brain which I can convert into an SDF or combination of volumes
>> in
>>> Houdini. I've actually got some DICOM slices of my own head but the
>> spacing
>>> is >2cm so there aren't really enough to extract a nice volume from it.
>> Then
>>> there is the whole issue of processing the DICOMs to get a nice
>>> representation of densities and different tissue types.
>>> 
>>> So if offhand anyone knows where to find something (any body
>>> part/animal/cool thing) which I could wrangle a houdini volume from
>> please
>>> let me know. This is for a personal project, not production and will be
>> made
>>> publicly available when I've got it working... It will be a bit of a
>>> surprise what I'm doing with it :D
>>> 
>>> cheers
>>> M
>>> _______________________________________________
>>> Sidefx-houdini-list mailing list
>>> Sidefx-houdini-list at sidefx.com
>>> https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list
>> 
>> _______________________________________________
>> Sidefx-houdini-list mailing list
>> Sidefx-houdini-list at sidefx.com
>> https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list
>> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Thu, 11 Aug 2011 10:15:20 +1000
> From: Martin Sawtell <martin at msawtell.com>
> Subject: Re: [Sidefx-houdini-list] MRI data / level set grids request
> To: sidefx-houdini-list at sidefx.com
> Message-ID:
>    <CABrzp6w2jTVkYYyKOwV7D8EKGNa5P4OXWxR5379bdVS6XLrUkg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Matt Ebb just put me onto this:
> http://www9.informatik.uni-erlangen.de/External/vollib/
> 
> So much to play with :)
> 
> 
> 
> On 11 August 2011 10:14, Martin Sawtell <martin at msawtell.com> wrote:
> 
>> Yes! Anything with lots of slices and some nice contrasts in colours/values
>> to make it easier to segment up/filter. Good stuff.
>> 
>> -M
>> 
>> 
>> 
>> On 11 August 2011 10:07, Stephen Tucker <stucker at allegrodigital.com>wrote:
>> 
>>> 
>>> Not MRI, but potentially useful if you took the frames
>>> 
>>> http://fstoppers.com/light-painting-with-1871-slices-of-a-corpse
>>> 
>>> 
>>>> Date: Thu, 11 Aug 2011 10:04:19 +1000
>>>> From: martin at msawtell.com
>>>> To: sidefx-houdini-list at sidefx.com
>>>> Subject: [Sidefx-houdini-list] MRI data / level set grids request
>>>> 
>>>> Hey all, I have a bit of an odd request; I'm hunting around for ideally
>>> a
>>>> scan of a brain which I can convert into an SDF or combination of
>>> volumes in
>>>> Houdini. I've actually got some DICOM slices of my own head but the
>>> spacing
>>>> is >2cm so there aren't really enough to extract a nice volume from it.
>>> Then
>>>> there is the whole issue of processing the DICOMs to get a nice
>>>> representation of densities and different tissue types.
>>>> 
>>>> So if offhand anyone knows where to find something (any body
>>>> part/animal/cool thing) which I could wrangle a houdini volume from
>>> please
>>>> let me know. This is for a personal project, not production and will be
>>> made
>>>> publicly available when I've got it working... It will be a bit of a
>>>> surprise what I'm doing with it :D
>>>> 
>>>> cheers
>>>> M
>>>> _______________________________________________
>>>> Sidefx-houdini-list mailing list
>>>> Sidefx-houdini-list at sidefx.com
>>>> https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list
>>> 
>>> _______________________________________________
>>> Sidefx-houdini-list mailing list
>>> Sidefx-houdini-list at sidefx.com
>>> https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list
>>> 
>> 
>> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Thu, 11 Aug 2011 10:25:19 +1000
> From: Ron Schab <ron.schab at gmail.com>
> Subject: Re: [Sidefx-houdini-list] MacBook Pro compatibility
> To: sidefx-houdini-list at sidefx.com
> Message-ID:
>    <CAJjzzvBY8XvfXSofuU_H0=-cQrexjSyty91CgQ+8ugjG+1=QiA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
>> From what I remember the openGL drivers for MacOSX are way outdated (unless
> the ones NVIDIA provides fixes this). Meaning no go with all the nice
> viewport enhancements of H11 and even moreso for the upcoming H12.  I don't
> know about the ones for/from ATI/AMD, but I would definitely check on that
> before comitting to an ATI.
> 
> The other big point would be to find out if H12's GPU exelaration is CUDA or
> OpenCL based/optimised.  Looking at the broader plattform for OpenCL one
> might suggest SESI would go with that, but then again CUDA seems quite a bit
> faster and in the H12 preview videos SESI mentions a Tesla (NVIDIA) which
> would definitely be quicker utilizing CUDA.  Maybe they support both?
> That's yet to be revealed.
> 
> However it'd definitely be a massive downer for me to go with ATI and then
> find out all the GPU enhanced sim features that are coming with H12 aren't
> running as well as they could be.
> 
> cheers
> Ron
> 
> 
> 
> On Thu, Aug 11, 2011 at 07:40, David Johnson <daveinengland at gmail.com>wrote:
> 
>> Using a quadro 4000 for mac on a mac pro with 32gb of ram, everything
>> rocks.
>> I was rendering a huge still (18000x5000) with lots of geometry in the
>> background while someone was painting on that huge image in photoshop and
>> it
>> was still about 35% faster than out 3 year old Dell.
>> 
>> That was the first project I've done on this machine, but so far I'm very
>> happy with it.
>> 
>> Dave
>> 
>> On Wednesday, August 10, 2011, Peter Bowmar <pbowmar at gmail.com> wrote:
>>> Yup, my CPU tests showed the Mantra renders (non graphical, to an
>>> image file) to be super fast, corresponding to CPU vintage. Graphics
>>> are the issue.
>>> 
>>> My understanding is that if you buy an Nvidia pro level card (Quadro
>>> 4000) you can get proper drivers from Nvidia and not rely on the
>>> relatively crap ones that Apple provide, but that is not something I
>>> know directly, it's 2nd hand info :)
>>> 
>>> Cheers,
>>> 
>>> Peter B
>>> 
>>> On 10 August 2011 13:38, Antoine Durr <antoinedurr at gmail.com> wrote:
>>>> We use Houdini on Mac Pros as well.  I think any apparent sluggishness
>> is
>> due to graphics cards and drivers.
>>>> 
>>>> -- Antoine
>>>> 
>>>> 
>>>> On Aug 10, 2011, at 1:25 PM, Larry Giunta wrote:
>>>> 
>>>>> I'll toss in that I've been using Houdini on a MacPro ( workstation,
>> not
>> book) for
>>>>> about a year now and I've been pretty happy with the results. We're not
>> doing
>>>>> feature work but a variety of spot, broadcast and corporate work in HD.
>>>>> 
>>>>> It's hard for me to compare speed directly with Linux because the Linux
>> boxes
>>>>> we have Houdini running on here are a bit older than the Mac ... so
>> it's
>> tough to compare.
>>>>> 
>>>>> Would not be surprised if it is in fact slower on OSX than Linux. But
>> the convenience of having
>>>>> all of my other Mac apps so handy ( Final Cut, AE, Pshop, tracking,
>> etc)
>> is a big plus for me.
>>>>> 
>>>>> The recent Final Cut news is concerning though .... tough to say where
>> that is all going.
>>>>> Holding on tight to my current cut for now.
>>>>> 
>>>>> Larry
>>>>> 
>>>>> --
>>>>> Larry Giunta
>>>>> Creative Director
>>>>> G Creative Studios
>>>>> (781)393-0200
>>>>> www.gcreativestudios.com
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Aug 10, 2011, at 1:41 PM, Nick Zutphen wrote:
>>>>> 
>>>>>> I have a Mac Book Pro which I keep for personal use, on which I have
>> Apprentice installed and for that purpose it works fine. Although you
>> should
>> keep in mind that Houdini is quite a bit slower on OSX (area of 10%). I
>> guess it depends what you're up to, I would consider it fine for .otl
>> development and that sort of things, but I wouldn't think about doing
>> serious simulation or render work on a Mac. I have to mention that if
>> Houdini was just as fast on OSX it would be a no brainer for me. For as
>> long
>> as Apple allows 'us' professional users, not sure if you are aware of
>> recent
>> activities around FinalCut, but it seems 'we' are going down the drain.
>>>>>> 
>>>>>> In case Jeff Wagner reads this, he might share his experiences with
>> Houdini on a Mac Book Pro, I happen to know that he carries one.
>>>>>> 
>>>>>> Cheers!
>>>>>> Nick van Zutphen
>>>>>> ----
>>>>>> http://www.nickvanzutphen.com
>>>>>> 
>>>>>> On Aug 10, 2011, at 7:25 PM, Martin Aufinger wrote:
>>>>>> 
>>>>>>> Thanks for your reply Antoine and Stefan.
>>>>>>> I might risk it then...
>>>>>>> 
>>>>>>> Imagine if the next generation had no optical drive, what a pain.
>>>>>>> 
>>>>>>> ----- Original Message -----
>>>>>>> From: "Antoine Durr" <antoinedurr at gmail.com>
>>>>>>> To: sidefx-houdini-list at sidefx.com
>>>>>>> Sent: Monday, 8 August, 2011 6:49:41 PM
>>>>>>> Subject: Re: [Sidefx-houdini-list] MacBook Pro compatibility
>>>>>>> 
>>>>>>> It's worked pretty reliably for me so far, but I've mostly been doing
>> OTL development, using VPN to grab a license token from the office.
>>>>>>> 
>>>>>>> -- Antoine
>>>>>>> 
>>>>>>> On Aug 8, 2011, at 6:40 AM, Martin Aufinger wrote:
>>>>>>> 
>>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> I was wondering if anyone has good or bad experiences with Houdini
>> on
>> current MacBookPro.
>>>>>>>> 
>>>>>>>> I am considering buying a new MacBookPro but want to make sure that
>> it works well with H11 (and H12?)
>>>>>>>> 
>>>>>>>> They are currently being shipped with AMD Radeon which from what I
>> read in the forums seems to work ok. Initial problems with OSX Lion appear
>> to be solved as well.
>>>>>>>> 
>>>>>>>> I am also wondering if it is worth waiting for the next MacBookPro
>> release and/or Houdini release to make sure that they work well together?
>> Opinions?
>>>>>>>> 
>>>>>>>> Any hints would be great.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> Martin
>>>>>>>> 
>>>>>>>> 
>>>>>>>> MacBookPro
>>>>> --
>>> Cheers,
>>> 
>>> Peter B
>>> 
>>> --No, I am not on Facebook.
>>> _______________________________________________
>>> Sidefx-houdini-list mailing list
>>> Sidefx-houdini-list at sidefx.com
>>> https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list
>>> 
>> _______________________________________________
>> Sidefx-houdini-list mailing list
>> Sidefx-houdini-list at sidefx.com
>> https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list
>> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Thu, 11 Aug 2011 00:07:47 -0400
> From: Mark Alexander <malexander at sidefx.com>
> Subject: Re: [Sidefx-houdini-list] MacBook Pro compatibility
> To: sidefx-houdini-list at sidefx.com
> Message-ID: <4E435593.1060107 at sidefx.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> On 08/10/2011 08:25 PM, Ron Schab wrote:
>> From what I remember the openGL drivers for MacOSX are way outdated (unless
>> the ones NVIDIA provides fixes this). Meaning no go with all the nice
>> viewport enhancements of H11 and even moreso for the upcoming H12.  I don't
>> know about the ones for/from ATI/AMD, but I would definitely check on that
>> before comitting to an ATI.
> 
> The H11 viewport works with ATI cards, but had issues with the Nvidia 
> cards until OSX 10.7 was released. I believe anti-aliasing is disabled 
> because GL_ARB_texture_multisample is unsupported. However, Apple's 
> drivers are a bit lower performance than AMD or Nvidia's own drivers, 
> though they are improving.
> 
> OSX 10.7 also comes with a new OpenGL 3.2 driver, which bumps them from 
> the GL2.1 support they have had for years. They chose to implement the 
> core profile of 3.2 however, so I'm not sure how that will play out yet.
> 
>> The other big point would be to find out if H12's GPU exelaration is CUDA or
>> OpenCL based/optimised.
> 
> While H12's GPU acceleration is OpenCL-based, Nvidia cards still hold 
> the compute crown over AMD. AMD just hasn't invested quite as much in 
> compute yet, though that is also changing with the next-gen AMD 
> architecture (2012?).
> 
> Cheers,
> M.
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Thu, 11 Aug 2011 14:48:35 +0200
> From: Magnus Pettersson <magnus at stormstudios.no>
> Subject: Re: [Sidefx-houdini-list] Geometry ROP HDA
> To: sidefx-houdini-list at sidefx.com
> Message-ID:
>    <CAAOuU_gQ+dN--qPSNSc5+bYHafvc8SmRyK5fAsjxY57cd=kn7g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> I dont find any way i can create a digital asset with 0 outputs in SOPs ,
> for now i have one with 1input and 1output and i just ignore the output,
> would be more intuitive tho if i could have the visual definition like the
> Rop Geometry Sop tho! :)
> 
> .................................................................................................
> Magnus Pettersson | Lead Effects TD
> Storm Studio AS
> www.stormstudios.no
> 
> 
> 
> 2011/7/7 Fran?ois Duchesneau <sidefx at trinix.ca>
> 
>> A guy at work created a custom camera by saving the definition of its otl
>> to a custom place and then added features inside it. I'm not sure this will
>> work with a Rop Geometry Sop since it's not like a container and I'm not
>> sure you have access to the interface.
>> 
>> Unfortunately when I try to do it at home with a non-commercial version it
>> crashes. Let me know if it's not working and I'll ask him more details.
>> 
>> Fran?ois
>> 
>> Magnus Pettersson wrote:
>> 
>>> Hello guys,
>>> 
>>> Im wondering if there is a way to get same look on a HDA as the
>>> ROP_geometry
>>> in SOPs (1 input and 0 outputs)?
>>> Im wanting to wrap the rop_geometry up in a digital asset to add some
>>> pipeline functionality when writing out stuff but i dont want any outputs
>>> going out from my hda, is this possible?
>>> 
>>> ..............................**..............................**
>>> ..............................**.......
>>> Magnus Pettersson | Lead Effects TD
>>> Storm Studio AS
>>> www.stormstudios.no
>>> ______________________________**_________________
>>> Sidefx-houdini-list mailing list
>>> Sidefx-houdini-list at sidefx.com
>>> https://lists.sidefx.com:443/**mailman/listinfo/sidefx-**houdini-list<https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list>
>>> 
>>> 
>>> 
>> ______________________________**_________________
>> Sidefx-houdini-list mailing list
>> Sidefx-houdini-list at sidefx.com
>> https://lists.sidefx.com:443/**mailman/listinfo/sidefx-**houdini-list<https://lists.sidefx.com:443/mailman/listinfo/sidefx-houdini-list>
>> 
> 
> 
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> 
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