measurements using MRI jpg images

[John Dufton]

Hello,

I have a question regarding measurements on mri images.

I have saved a number of images as jpg images.  The measurements on these
jpg images do not seem to correspond to measurements on the workstation.  
This did not occur previously when I saved the images as dicom images.  
Could someone explain to me why this might be and if there is a solution?

Specifically, I have previously saved a number of dicom images and then
loaded these onto imagej.  The measurements that I took corresponded well
to the measurements taken on the workstation.
Now, on a different workstation that uses different software (impax) I
have saved images as jpg images because this seems to be the default, and
when I load these images to imagej the measurements do not correspond.

Any help would be much appreciated,
Thanks,
John

[Gabriel Landini]

On Sunday 15 October 2006 06:43, John Dufton wrote:
> I have a question regarding measurements on mri images.
> I have saved a number of images as jpg images.  The measurements on these
> jpg images do not seem to correspond to measurements on the workstation.

Hi,
Jpeg compressed images should not be used for serious imaging purposes.
The compression in the jpegs is lossy, so I guess that you may be measuring
some amount of artifacts rather than the data.

Instead, you can save your images as Tiff or Png.

Cheers.

Gabriel

[Divya Rathore]

> On Sunday 15 October 2006 06:43, John Dufton wrote:
>> I have a question regarding measurements on mri images.
>> I have saved a number of images as jpg images.  The measurements on
>> these
>> jpg images do not seem to correspond to measurements on the workstation.
>
> Hi,
> Jpeg compressed images should not be used for serious imaging purposes.
> The compression in the jpegs is lossy, so I guess that you may be
> measuring some amount of artifacts rather than the data.
>
> Gabriel
>

I completely second Gabriel. Jpeg is not the format for serious
quantitations in MRI.

In case you are using Windows, you can try 'HeaderCorrection.exe' program
that I have made to chop off the header data in DICOMs and save image data
as separate files. Later use ImageJ to read them as Raw files.

The link is:
http://home.iitk.ac.in/~rksr/softwares/

Step 1: choose single/multiple file(s)
Step 2: choose output folder where you want the data to be saved.
Step 3: You would be knowing the width and height of the data. Feed it.
DICOM is normally 2 byte data. So 'Bytes per pixel' remain 2.
Step 4: Optional. Can be zero. Default is 8432.

Press Process button and you are through.

Later use ImageJ to open the generated files.
File >> Import >> Raw >> Selelct the output folder as in Step 2.
In the Dialog that shows up use following params:

Image Type: 16 Bit Unsigned.
Offset to first image: As in step 4 above.
rest of the parameters depends on the data.


hope that helps..

cheers,

- Divya Rathore
Research Engineer,
Deptt of Mathematics and Statistics,
IIT Kanpur,
INDIA.

[Gino Canessa]

My guess would be that there is no calibration reference for the JPEG images
(e.g., it is measuring pixels), whereas the DICOM images have calibration so
that measurements can be converted into more useful numbers (e.g., mm).

If you are just measuring pixels on both, as Gabriel said, there are
artifacts introduced by the JPEG conversion.


All of this assumes, of course, that by saying  "jpg," you mean an actual
JPEG, instead of a JPEG compressed DICOM.  If you are using a JPEG
compressed DICOM image, and the compression was set to lossless, there
should be no differences.

Hope this helps,

    Gino


P.s., Just like to re-enforce Gabriel's mention that JPEG images should not
be used for analysis of anything (again, barring the lossless types common
in DICOM, et all).





On 10/15/06 4:54 PM, "Gabriel Landini" <[hidden email]> wrote:

> On Sunday 15 October 2006 06:43, John Dufton wrote:
>> I have a question regarding measurements on mri images.
>> I have saved a number of images as jpg images.  The measurements on these
>> jpg images do not seem to correspond to measurements on the workstation.
>
> Hi,
> Jpeg compressed images should not be used for serious imaging purposes.
> The compression in the jpegs is lossy, so I guess that you may be measuring
> some amount of artifacts rather than the data.
>
> Instead, you can save your images as Tiff or Png.
>
> Cheers.
>
> Gabriel

--
Gino Canessa
 
Software Engineering Corporation (SENCOR)
7900 International Drive - Suite 305
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web:      www.sencorsoft.com or www.sencor.com
 
email:    [hidden email]
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support:  [hidden email]
 

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[John Dufton]

Thanks gino,

I think this is the problem.  the images i have lack the calibration.

And thanks to everyone else regarding the use of jpg images for measuring.

Is there is a way to convert these jpg to dicom or is that not possible?


thanks again.

>From: Gino Canessa <[hidden email]>
>Reply-To: ImageJ Interest Group <[hidden email]>
>To: [hidden email]
>Subject: Re: measurements using MRI jpg images
>Date: Sun, 15 Oct 2006 20:41:28 -0500
>
>My guess would be that there is no calibration reference for the JPEG
>images
>(e.g., it is measuring pixels), whereas the DICOM images have calibration
>so
>that measurements can be converted into more useful numbers (e.g., mm).
>
>If you are just measuring pixels on both, as Gabriel said, there are
>artifacts introduced by the JPEG conversion.
>
>
>All of this assumes, of course, that by saying  "jpg," you mean an actual
>JPEG, instead of a JPEG compressed DICOM.  If you are using a JPEG
>compressed DICOM image, and the compression was set to lossless, there
>should be no differences.
>
>Hope this helps,
>
>     Gino
>
>
>P.s., Just like to re-enforce Gabriel's mention that JPEG images should not
>be used for analysis of anything (again, barring the lossless types common
>in DICOM, et all).
>
>
>
>
>
>On 10/15/06 4:54 PM, "Gabriel Landini" <[hidden email]> wrote:
>
> > On Sunday 15 October 2006 06:43, John Dufton wrote:
> >> I have a question regarding measurements on mri images.
> >> I have saved a number of images as jpg images.  The measurements on
>these
> >> jpg images do not seem to correspond to measurements on the
>workstation.
> >
> > Hi,
> > Jpeg compressed images should not be used for serious imaging purposes.
> > The compression in the jpegs is lossy, so I guess that you may be
>measuring
> > some amount of artifacts rather than the data.
> >
> > Instead, you can save your images as Tiff or Png.
> >
> > Cheers.
> >
> > Gabriel
>
>--
>Gino Canessa
>
>Software Engineering Corporation (SENCOR)
>7900 International Drive - Suite 305
>Bloomington, MN 55425
>
>web:      www.sencorsoft.com or www.sencor.com
>
>email:    [hidden email]
>voice:    952.854.7175 ext. 204
>fax:      [phone]
>support:  [hidden email]
>
>
>CONFIDENTIALITY NOTICE
>
>This message and any included attachments are from SENCOR and
>are intended only for the addressee. The information
>contained in this message is confidential and may constitute
>inside or non-public information under international,
>federal, or state securities laws.  Unauthorized forwarding,
>printing, copying, distribution, or use of such information
>is strictly prohibited and may be unlawful.  If you are not
>the intended recipient, please promptly delete this message
>and notify the sender of the delivery error by e-mail or
>calling SENCOR's corporate offices in Bloomington,
>Minnesota, U.S.A. at 952.854.7175.  Thank you.
>

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[Gabriel Landini]

On Monday 16 October 2006 03:03, John Dufton wrote:
> I think this is the problem.  the images i have lack the calibration.

Hi,
Even if the images were calibrated, when the image is jpeg compressed, your
pixel values are not the original ones and you will get inconsistent results.

> And thanks to everyone else regarding the use of jpg images for measuring.
> Is there is a way to convert these jpg to dicom or is that not possible?

No, unfortunately the jpeg compression is one way. When encoding, it throws
away the data that is not very obvious to the eye (but it is very obvious to
any imaging procedure). That is how it achieves small file sizes.

The real data is gone forever and one is left with something that "looks like
the original" and takes less space (which is good for the web and the
occasional photo album, but not for doing any quantitative analysis).

You should be better off by converting your dicom images to tiff or png.
Sure one can specify no compression in a jpeg file, so it saves all the data,
but why to use uncompressed jpeg format, when tiff and png can do non-lossy
compression if necessary?

Cheers,

Gabriel

[Michael A. Miller]

>>>>> "Gabriel" == Gabriel Landini <[hidden email]> writes:

    > You should be better off by converting your dicom images to
    > tiff or png.  Sure one can specify no compression in a jpeg
    > file, so it saves all the data, but why to use uncompressed
    > jpeg format, when tiff and png can do non-lossy compression
    > if necessary?

He may be even better off not doing the conversion at all.  DICOM
files contain a large amount of meta data that cannot be
incorporated into tiff or png or any other "picture" format, even
though the pixel intensities may be the same in each format.
Medical image data is rarely (never?) just pixel data, and
therefore image formats designed for primarily pixel data will
always fall short.

As is sometimes said in the medical imaging community "to convert
IS to delete."  I think this originally came from remarks
accompanying the (X)MedCon source, which also says "!! ALWAYS
PRESERVE YOUR ORIGINAL DATA !!" - also very good advice.  Even
converting among the various medical image data formats is not
typically possible without deleting some meta data.

Mike