[Insight-users] Urgent: Strange dicom imageIO

[Miller, James V (GE, Research)]

Markus,

This is the difficulty in working with DICOM in a generic fashion.

When ITK reads a DICOM file/series, it applies the slope/intersept to the
data to so that the intensity values appear to ITK filters in the units
of the scanner (HU for CT, counts for PET, etc.).  This allows you to 
operate on the data in the proper units.  This is particularly important
for PET images since the each slice in a series usually have a different
slope value.  In the PET case, the slope HAS to be applied to get the
data from all the slices to be in the same units.  This is all easy to
do when reading DICOM.

When writing DICOM, ITK does not undo this mapping.  This is the problem
that you are seeing.  We have been struggling on how to address this issue.
If the slope/intersept are specified in the meta data, we put these values
into the DICOM header.  But we do not unapply this pixel transform. So if 
you read this data back in, it essentially has had the slope/intersept applied
twice!

At issue is that the writer doesn't know whether these offsets/scales have
already been applied to the data and the writer just needs to put these
values in the header or whether these offsets/scales need to be applied
by the writer AND the values need to be placed in the header.  We need
to work on this.

A workaround is place a ShiftScaleImageFilter before the writer to apply
the pixel manipulation.  This way the writer is provided with data that
has already been transformed to how it would appear on disk.

Of course, when we fix this issue, your shift/scale calculation will have
to be removed to avoid applying it twice.

In summary, DICOM is more difficult to produce than the other formats
that ITK supports.  In particular, the application needs to understand
DICOM tags and meta data dictionary in order to produce DICOM.  One of the
things we want to do is make ITK generate DICOM more reliably.  This includes
identifying the subset of tags that have to be present in order to import
the data into commerical DICOM compliant applications.

Jim




-----Original Message-----
From: insight-users-bounces+millerjv=crd.ge.com at itk.org
[mailto:insight-users-bounces+millerjv=crd.ge.com at itk.org]On Behalf Of
Markus Weigert
Sent: Wednesday, May 10, 2006 5:33 PM
To: insight-users at itk.org
Subject: [Insight-users] Urgent: Strange dicom imageIO


Hi,

today I encountered a strange  problem with dicom ImageIO:

After reading a dicom series of  CT - files and displaying the volume with
GLTwoImageSliceView (from insight applications), everything is fine.
The range of the values is -1024 up to 3071, just as it should be.

But after writing the serie again to dicom slices and reading these slices,
the range is now -2048 to 2047, so there seems to be a shift.
I don't understand this, because I didn't change anything in the 
MetaDataDictionaryArray.

Has anybody an idea what could cause this shifting of image values?

Regards,
Markus

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