Single DICOm file - Volume loading

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Single DICOm file - Volume loading

mitchcud
Hi all,

Is it possible to load a single DICOM file as a volume? I have just received a DVD of what should be a series of microCT scans as a single file. File is approximately 900 MB in size

Thanks,

Mitch
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

Steve Pieper
Hi Mitch -

If a volume is embedded in a single dicom file using the 'dicom multi-frame' standard then slicer should be able to load it fine.  This was added about a year ago to support newer MR scanners.  What happens when you try to load the file?

-Steve

On Mon, May 23, 2011 at 5:01 AM, mitchcud <[hidden email]> wrote:
Hi all,

Is it possible to load a single DICOM file as a volume? I have just received
a DVD of what should be a series of microCT scans as a single file. File is
approximately 900 MB in size

Thanks,

Mitch

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Re: Single DICOm file - Volume loading

mitchcud
It won't load the volume for me. It says the 'file does not match standard volume formats'

I can access the metadata through MATLAB, i.e. through 'dicominfo' function (I've attached in text file). When I go as far as trying to read it in, MATLAB crashes out and says I don't have enough memory, bear in mind that I'm working off Intel Core 2 Duo E8400 (3.0 GHZ) w/ 4GB RAM. And I'm using Slicer 3.6.3.

The original CT scans were taken with a Scanco UCT40 MicroCT Scanner, whose output is the .ISQ file. I asked my friend for DICOM files and this is what I got!

Any thoughts?  



Metadata.txt
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

Andras Lasso
If you retrieve the data from the scanner using a DICOM store client (such
as the storescp tool in DCMTK) then you can remove the
EnhancedCTImageStorage (the multi-frame image) format from the accepted SOP
classes by editing the storescp configuration file. Then the scanner will
probably negotiate the traditional (single frame per image file) format with
the DICOM store application, which format should be supported by Slicer,
Matlab, etc.

If this doesn't work or you prefer to work with multi-frame image files then
you need to send a few sample files to GDCM developers for analysis.

Andras

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of mitchcud
Sent: 2011-May-23 12:41 PM
To: [hidden email]
Subject: Re: [slicer-users] Single DICOm file - Volume loading

It won't load the volume for me. It says the 'file does not match standard
volume formats'

I can access the metadata through MATLAB, i.e. through 'dicominfo' function
(I've attached in text file). When I go as far as trying to read it in,
MATLAB crashes out and says I don't have enough memory, bear in mind that
I'm working off Intel Core 2 Duo E8400 (3.0 GHZ) w/ 4GB RAM. And I'm using
Slicer 3.6.3.

The original CT scans were taken with a Scanco UCT40 MicroCT Scanner, whose
output is the .ISQ file. I asked my friend for DICOM files and this is what
I got!

Any thoughts?  



http://slicer-users.65878.n3.nabble.com/file/n2975995/Metadata.txt
Metadata.txt

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Re: Single DICOm file - Volume loading

Mathieu Malaterre
Hi,

On Tue, May 24, 2011 at 4:06 AM, Andras Lasso <[hidden email]> wrote:
> If you retrieve the data from the scanner using a DICOM store client (such
> as the storescp tool in DCMTK) then you can remove the
> EnhancedCTImageStorage (the multi-frame image) format from the accepted SOP
> classes by editing the storescp configuration file. Then the scanner will
> probably negotiate the traditional (single frame per image file) format with
> the DICOM store application, which format should be supported by Slicer,
> Matlab, etc.

This is the first time I hear this. This sound like a pretty good
feature, which scanner implements this ?

> If this doesn't work or you prefer to work with multi-frame image files then
> you need to send a few sample files to GDCM developers for analysis.

Basically you can even do the test yourself, run gdcminfo and it will
display the image information. Please note that Enhanced CT Image
Storage is a Multi Frame storage class which is different from the 3D
storage expected by ITK/VTK and other (multiframe only imply
consistant cols/rows, but you could have say multiple orientation).

HTH
--
Mathieu
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Re: Single DICOm file - Volume loading

Steve Pieper
In reply to this post by mitchcud
Any chance you can post an example file in this format for testing?

On Mon, May 23, 2011 at 12:41 PM, mitchcud <[hidden email]> wrote:
It won't load the volume for me. It says the 'file does not match standard
volume formats'

I can access the metadata through MATLAB, i.e. through 'dicominfo' function
(I've attached in text file). When I go as far as trying to read it in,
MATLAB crashes out and says I don't have enough memory, bear in mind that
I'm working off Intel Core 2 Duo E8400 (3.0 GHZ) w/ 4GB RAM. And I'm using
Slicer 3.6.3.

The original CT scans were taken with a Scanco UCT40 MicroCT Scanner, whose
output is the .ISQ file. I asked my friend for DICOM files and this is what
I got!

Any thoughts?



http://slicer-users.65878.n3.nabble.com/file/n2975995/Metadata.txt
Metadata.txt

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Re: Single DICOm file - Volume loading

Andras Lasso
In reply to this post by Mathieu Malaterre

I assume that the traditional single-file-per-frame format should be
supported by most (all?) of the scanners that supports the new
single-file-per-image format. I've specifically tested this on a Philips
Achieva 3.0 MRI scanner with DCMTK. If the enhanced MRI storage SOP class
was present in the storescp config file then I received the image in one
single file. If the enhanced MRI SOP storage class was not present, then I
received the image in multiple files.

Andras

-----Original Message-----
From: Mathieu Malaterre [mailto:[hidden email]]
Sent: 2011-May-24 3:11 AM
To: Andras Lasso
Cc: mitchcud; [hidden email]
Subject: Re: [slicer-users] Single DICOm file - Volume loading

Hi,

On Tue, May 24, 2011 at 4:06 AM, Andras Lasso <[hidden email]> wrote:
> If you retrieve the data from the scanner using a DICOM store client (such
> as the storescp tool in DCMTK) then you can remove the
> EnhancedCTImageStorage (the multi-frame image) format from the accepted
SOP
> classes by editing the storescp configuration file. Then the scanner will
> probably negotiate the traditional (single frame per image file) format
with
> the DICOM store application, which format should be supported by Slicer,
> Matlab, etc.

This is the first time I hear this. This sound like a pretty good
feature, which scanner implements this ?

> If this doesn't work or you prefer to work with multi-frame image files
then
> you need to send a few sample files to GDCM developers for analysis.

Basically you can even do the test yourself, run gdcminfo and it will
display the image information. Please note that Enhanced CT Image
Storage is a Multi Frame storage class which is different from the 3D
storage expected by ITK/VTK and other (multiframe only imply
consistant cols/rows, but you could have say multiple orientation).

HTH
--
Mathieu

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Re: Single DICOm file - Volume loading

mitchcud
In reply to this post by Steve Pieper
Well I don't think so, as all I have is the one 900MB file...?
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

Steve Pieper
If the image data is non-confidential, you could put it on a public web site (e.g. sign up for dropbox and put it in the Public folder) and then send us a link.  Or maybe you can get a smaller example file that shows the same issue?

-Steve

On Tue, May 24, 2011 at 1:07 PM, mitchcud <[hidden email]> wrote:
Well I don't think so, as all I have is the one 900MB file...?

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Re: Single DICOm file - Volume loading

mitchcud
Okay, I have it uploaded it my Dropbox account.

Hope this works:

http://dl.dropbox.com/u/26697713/tooth_scan.dcm
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

Steve Pieper
Hi Mitch -

Thanks for posting that scan - the good news is that this data does load into my version of slicer.  So this file is a standard multiframe dicom volume file.  The difference may be that I'm using a 64 bit build of slicer (on linux 64 host).  Are you using a 64 bit windows OS?  if you are using the win32 slicer build it must be running out of memory with the big file.  If so you can try the 64 bit build of slicer3 that's in the Snapshots portion of the slicer.org downloads page.

I've attached a picture of what I get with that data after making a model.

Best,
Steve

On Wed, May 25, 2011 at 9:46 AM, mitchcud <[hidden email]> wrote:
Okay, I have it uploaded it my Dropbox account.

Hope this works:

http://dl.dropbox.com/u/26697713/tooth_scan.dcm

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Re: Single DICOm file - Volume loading

mitchcud
That must be it so Steve.

I have only got a 32 bit version but I'm gonna hunt extra memory and the 64 bit version

Thanks for you help,

Mitch
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

mitchcud
In reply to this post by Steve Pieper
Steve,

I've upgraded my PC (now w/16GB RAM & 64bit OS), I've managed to get a 3D model up and running but the outputted STL file is absolutely enormous, around 6.5GB...is that what you got when you assembled the model?

Is there any way to optimise (or tidy them up) these files? I'm exporting to a 32 bit FEA software so I'll be limited with the RAM I can play around with!

Thanks
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

Steve Pieper
Hi Mitch -

Sounds like good progress - definitely there are many ways to make
smaller models.  Here are a few things that come to mind:

- You can use the Resample Volume module to reduce the size of the input volume

- You may have a lot of internal structure that you don't want in the
model (like isolated dots of noise).  You can use the Remove Islands
tool in the Editor to clean these up.  Or you can use one of the tools
in Filters->Denoising to reduce the noise before segmenting.

- You can adjust the parameters on the Model Maker (rather than using
the defaults built into the Editor)

- You can use the Surface Toolbox to post-process the models (apply
further smoothing/decimation).

Hopefully one or more of those will work for you.  STL is a very
verbose ascii format, so even if the file is big, it may not be so
large when loaded into your FEA app.

Good luck,
Steve


On Fri, Jun 3, 2011 at 8:31 AM, mitchcud <[hidden email]> wrote:

> Steve,
>
> I've upgraded my PC (now w/16GB RAM & 64bit OS), I've managed to get a 3D
> model up and running but the outputted STL file is absolutely enormous,
> around 6.5GB...is that what you got when you assembled the model?
>
> Is there any way to optimise (or tidy them up) these files? I'm exporting to
> a 32 bit FEA software so I'll be limited with the RAM I can play around
> with!
>
> Thanks
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Single-DICOm-file-Volume-loading-tp2974519p3019439.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
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>
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Re: Single DICOm file - Volume loading

Kikinis, Ron,M.D.
Hi,

I tried to follow the spirit of Steves recommendation. By using crop
volume to crop and downsample, and then doing some simple things in the
editor such as island removal, save island and closing (dilation and
erosion combo), I got an STL file of 104mb.

Ron

On 6/3/11 8:53 AM, Steve Pieper wrote:

> Hi Mitch -
>
> Sounds like good progress - definitely there are many ways to make
> smaller models.  Here are a few things that come to mind:
>
> - You can use the Resample Volume module to reduce the size of the input volume
>
> - You may have a lot of internal structure that you don't want in the
> model (like isolated dots of noise).  You can use the Remove Islands
> tool in the Editor to clean these up.  Or you can use one of the tools
> in Filters->Denoising to reduce the noise before segmenting.
>
> - You can adjust the parameters on the Model Maker (rather than using
> the defaults built into the Editor)
>
> - You can use the Surface Toolbox to post-process the models (apply
> further smoothing/decimation).
>
> Hopefully one or more of those will work for you.  STL is a very
> verbose ascii format, so even if the file is big, it may not be so
> large when loaded into your FEA app.
>
> Good luck,
> Steve
>
>
> On Fri, Jun 3, 2011 at 8:31 AM, mitchcud<[hidden email]>  wrote:
>> Steve,
>>
>> I've upgraded my PC (now w/16GB RAM&  64bit OS), I've managed to get a 3D
>> model up and running but the outputted STL file is absolutely enormous,
>> around 6.5GB...is that what you got when you assembled the model?
>>
>> Is there any way to optimise (or tidy them up) these files? I'm exporting to
>> a 32 bit FEA software so I'll be limited with the RAM I can play around
>> with!
>>
>> Thanks
>>
>> --
>> View this message in context: http://slicer-users.65878.n3.nabble.com/Single-DICOm-file-Volume-loading-tp2974519p3019439.html
>> Sent from the slicer-users mailing list archive at Nabble.com.
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
>>
> _______________________________________________
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> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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--
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Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis

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Re: Single DICOm file - Volume loading

mitchcud
Ron,

Could you elaborate on the 'dilation and erosion combo'

I think I'm getting there with the model finally!

Thanks,
Mitch
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

mitchcud
Hi all,

I've got a model up and running. (see below)

Can anyone explain the 'pock marks' along the surface of the tooth?
(particularly Steve and Ron, your models don't seem to have these)

I've a feeling that it has something to with the Smoothing and Decimation applied in the Model Maker

Thanks

Mitch
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)
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Re: Single DICOm file - Volume loading

Kikinis, Ron,M.D.
Its likely an effect of the noise in your data. Attached is a volume
rendering showing similar surface patterns.
btw: You can use island removal and save island to further clean the
label maps.

On 6/8/11 12:30 PM, mitchcud wrote:

> Hi all,
>
> I've got a model up and running. (see below)
>
> Can anyone explain the 'pock marks' along the surface of the tooth?
> (particularly Steve and Ron, your models don't seem to have these)
>
> I've a feeling that it has something to with the Smoothing and Decimation
> applied in the Model Maker
>
> Thanks
>
> Mitch
> http://slicer-users.65878.n3.nabble.com/file/n3039769/tooth_mc_20110608.png
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Single-DICOm-file-Volume-loading-tp2974519p3039769.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis

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Re: Single DICOm file - Volume loading

Steve Pieper
Yes, I agree this is noise.

I'm thinking that one of the edge preserving filters (the Anisotropic
Diffusion filters under Denoising) would work well for this data.  I'd
suggest extracting a small volume (using CropVolume) to experiment
with.  Given that you really want a strong boundary between tooth and
air you could be pretty aggressive with the parameters without losing
much of the detail you are trying to preserve.

Let us know how it works out....

Best,
Steve

On Thu, Jun 9, 2011 at 8:26 AM, Ron Kikinis <[hidden email]> wrote:

> Its likely an effect of the noise in your data. Attached is a volume
> rendering showing similar surface patterns.
> btw: You can use island removal and save island to further clean the label
> maps.
>
> On 6/8/11 12:30 PM, mitchcud wrote:
>>
>> Hi all,
>>
>> I've got a model up and running. (see below)
>>
>> Can anyone explain the 'pock marks' along the surface of the tooth?
>> (particularly Steve and Ron, your models don't seem to have these)
>>
>> I've a feeling that it has something to with the Smoothing and Decimation
>> applied in the Model Maker
>>
>> Thanks
>>
>> Mitch
>>
>> http://slicer-users.65878.n3.nabble.com/file/n3039769/tooth_mc_20110608.png
>>
>> --
>> View this message in context:
>> http://slicer-users.65878.n3.nabble.com/Single-DICOm-file-Volume-loading-tp2974519p3039769.html
>> Sent from the slicer-users mailing list archive at Nabble.com.
>> _______________________________________________
>> slicer-users mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> To unsubscribe: send email to
>> [hidden email] with unsubscribe as the
>> subject
>
> --
> Ron Kikinis, M.D.,
> Robert Greenes Distinguished Director of Biomedical Informatics
> Professor of Radiology, Harvard Medical School
> Director, Surgical Planning Laboratory
> http://www.spl.harvard.edu/~kikinis
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
>
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Re: Single DICOm file - Volume loading

mitchcud
Hi

Just in relation to the model I'm building, I've built to a fine degree of accuracy now I think. Using the Label Map Smoothing module really helped. I now have a VTK model of about 70MB so that is ideal.

My final question is related to the FE meshing module. It seems to be crashing very regularly when I'm in the middle of a zoom or pan operation.
Any explanation / solution for this?

Thanks
Mitch Cuddihy

Department of Civil Engineering
National University of Ireland (Cork)