[ITK] Dicom read error

[Sean Sethi]

Hi Bill,

I shared this information with our developer. We already rewrite image
position in our processed data. Can you please look at the data sets which
I linked?

And I have to disagree about the display of the image. I attached image
showing ITK's display of dicoms before and after I renamed the filenames
only. You can see the beforehand image where the discontinuities are in
coronal and sagittal view. Those headers should be the same since I did not
change them.

Sean

On Thu, Jul 6, 2017 at 2:59 PM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:

> It's uses the image position patient tag to determine slice location.
> Image spacing is not used. Also, it does not use the name of them for
> ordering. Once again it uses Ipp.
>
> This is common practice in medical image processing software.
>
> Sent from my iPad
>
> On Jul 6, 2017, at 12:11 PM, Sean Sethi <sethisea at gmail.com> wrote:
>
> Hi everyone,
>
> I am encountering a dicom read issue with data that was processed using a
> collapsing filter by our software. The original data
> <https://www.dropbox.com/s/wsf6rb3edoritj9/02-MPRAGE%20T1.zip?dl=0> is
> 0.5x0.5x1 mm^3 which is collapsed to a dataset of  1x1x2 mm^3.
> <https://www.dropbox.com/s/7f34ahrmho938gb/KCROP1X1X2.zip?dl=0>
>
> The first error that is noticed is the data appear squished axially, and
> the slice thickness is incorrectly read, even though the header file has
> the correct information. (slice thickness=2, spacing between slices=2).
>
> The second error that I see is due to it incorrectly reading the numbering
> of the dicoms. It shows every 11th or so image as out of order, which is
> coming from reading the numbers in order of 1, 10, 11, 12 etc instead of 1,
> 2,3. When the files are number 01, 02, 03, the issue is corrected, but
> image still appears squashed.
>
> Both the issues are also corrected when the collapsed data is converted to
> NIFTI. So my question is how should we write our DICOM files so they are
> read correctly? Are the thicknesses and spacings computed from other
> tag(s)?
>
> Thank you for consideration,
>
> Sean
>
>
> --
> Sean Sethi, M.S.
> Research, The MRI Institute for Biomedical Research
> Data processing, Magnetic Resonance Innovations, Inc.
> 440 East Ferry Street, Unit #1
> Detroit, MI 48202
> (313) 758-0065  - Tel
> (313) 758-0068 - Fax
> sethisea at gmail.com
> http://www.mrimaging.com/
> http://www.mrinnovations.com
>
> _______________________________________________
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>
>


-- 
Sean Sethi, M.S.
Research, The MRI Institute for Biomedical Research
Data processing, Magnetic Resonance Innovations, Inc.
440 East Ferry Street, Unit #1
Detroit, MI 48202
(313) 758-0065  - Tel
(313) 758-0068 - Fax
sethisea at gmail.com
http://www.mrimaging.com/
http://www.mrinnovations.com
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