Dicom to analyze conversion -> orientation

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Dicom to analyze conversion -> orientation

pouria mojabi
Dear Experts,

Hope this email finds you all well.

I am struggling with Image Position(0020, 0032) and Image Orientation(0020, 0037) in Dicom images for a while now. I have two conversion tools that spit different results when they perform conversion from Dicom to Analyze image.

Debabler from LONI, outputs Analyze image in transverse unflipped format. [176 x 256 x 256] and the one that SPM provides gives me coronal unflipped with [256 x 256 x 176] being the dimension.

My Dicom's direction cosine is :
0.06     0.09     -0.12     0.03     -0.12     -0.99
and the Image position is:
-11.2     -123.2 130.29

Does slicer provide a conversion tool for regular Dicoms and Dicom mosaic?

I would really appreciate any advice on what the truth is, or better say, which one i should stick with. any pointers on this topic is also highly appreciate it. I need to understand the mechanics of such conversions and why orientation has a vicarious nature.

Thank you very much indeed
Pouria


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Re: Dicom to analyze conversion -> orientation

pieper
Administrator
Hi Pouria -

If this you have non-mosaic dicom data, you should be able to load into
slicer and save as analyze.  I'm not sure what orientation the pixel
data will be, but the directions and origins should be correct and
faithful to the dicom data (in general slicer will try to preserve the
voxel orientation too, but there may be constraints in the analyze writer).

This page describes the coordinate systems in general:

http://www.slicer.org/slicerWiki/index.php/Coordinate_systems

For mosaic data, you may need to use this tool:

http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.6

it is developed for use with diffusion imaging data, but might be useful
for you.

If you need more info on diffusion, check here:

http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format

Best,
Steve

p.s. don't worry - everyone has trouble with the coordinate systems!

On 12/15/2010 05:08 PM, pouria mojabi wrote:

> Dear Experts,
>
> Hope this email finds you all well.
>
> I am struggling with Image Position(0020, 0032) and Image
> Orientation(0020, 0037) in Dicom images for a while now. I have two
> conversion tools that spit different results when they perform
> conversion from Dicom to Analyze image.
>
> Debabler from LONI, outputs Analyze image in transverse unflipped
> format. [176 x 256 x 256] and the one that SPM provides gives me coronal
> unflipped with [256 x 256 x 176] being the dimension.
>
> My Dicom's direction cosine is :
> 0.06 0.09 -0.12 0.03 -0.12 -0.99
> and the Image position is:
> -11.2 -123.2 130.29
>
> Does slicer provide a conversion tool for regular Dicoms and Dicom mosaic?
>
> I would really appreciate any advice on what the truth is, or better
> say, which one i should stick with. any pointers on this topic is also
> highly appreciate it. I need to understand the mechanics of such
> conversions and why orientation has a vicarious nature.
>
> Thank you very much indeed
> Pouria
>
>
>
> _______________________________________________
> 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]
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Re: Dicom to analyze conversion -> orientation

Xiaodong Tao-3
In reply to this post by pouria mojabi
Hello Pouria,

You can try the module DicomToNrrdConverter in Slicer3.

For mosaic format, 0020|0032 tag in dicom header may not be the real
image position patient.

Let me know how this works for you.

Xiaodong

On Wed, Dec 15, 2010 at 5:08 PM, pouria mojabi <[hidden email]> wrote:

> Dear Experts,
>
> Hope this email finds you all well.
>
> I am struggling with Image Position(0020, 0032) and Image Orientation(0020,
> 0037) in Dicom images for a while now. I have two conversion tools that spit
> different results when they perform conversion from Dicom to Analyze image.
>
> Debabler from LONI, outputs Analyze image in transverse unflipped format.
> [176 x 256 x 256] and the one that SPM provides gives me coronal unflipped
> with [256 x 256 x 176] being the dimension.
>
> My Dicom's direction cosine is :
> 0.06     0.09     -0.12     0.03     -0.12     -0.99
> and the Image position is:
> -11.2     -123.2 130.29
>
> Does slicer provide a conversion tool for regular Dicoms and Dicom mosaic?
>
> I would really appreciate any advice on what the truth is, or better say,
> which one i should stick with. any pointers on this topic is also highly
> appreciate it. I need to understand the mechanics of such conversions and
> why orientation has a vicarious nature.
>
> Thank you very much indeed
> Pouria
>
>
> _______________________________________________
> 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
>



--
Xiaodong Tao
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Re: Dicom to analyze conversion -> orientation

Isaiah Norton-3
If the other suggestions don't work, MRIcro will work with at least (confirmed myself) Siemens mosaic data for conversion to analyze or nifti (MRIcroN):

http://www.cabiatl.com/mricro/mricro/index.html

-isaiah

On Wed, Dec 15, 2010 at 6:03 PM, Xiaodong Tao <[hidden email]> wrote:
Hello Pouria,

You can try the module DicomToNrrdConverter in Slicer3.

For mosaic format, 0020|0032 tag in dicom header may not be the real
image position patient.

Let me know how this works for you.

Xiaodong

On Wed, Dec 15, 2010 at 5:08 PM, pouria mojabi <[hidden email]> wrote:
> Dear Experts,
>
> Hope this email finds you all well.
>
> I am struggling with Image Position(0020, 0032) and Image Orientation(0020,
> 0037) in Dicom images for a while now. I have two conversion tools that spit
> different results when they perform conversion from Dicom to Analyze image.
>
> Debabler from LONI, outputs Analyze image in transverse unflipped format.
> [176 x 256 x 256] and the one that SPM provides gives me coronal unflipped
> with [256 x 256 x 176] being the dimension.
>
> My Dicom's direction cosine is :
> 0.06     0.09     -0.12     0.03     -0.12     -0.99
> and the Image position is:
> -11.2     -123.2 130.29
>
> Does slicer provide a conversion tool for regular Dicoms and Dicom mosaic?
>
> I would really appreciate any advice on what the truth is, or better say,
> which one i should stick with. any pointers on this topic is also highly
> appreciate it. I need to understand the mechanics of such conversions and
> why orientation has a vicarious nature.
>
> Thank you very much indeed
> Pouria
>
>
> _______________________________________________
> 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
>



--
Xiaodong Tao
_______________________________________________
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: Dicom to analyze conversion -> orientation

pouria mojabi
Thank you very much all for the comments. I am really grateful
Thanks
P

On 12/15/2010 8:20 PM, Isaiah Norton wrote:
If the other suggestions don't work, MRIcro will work with at least (confirmed myself) Siemens mosaic data for conversion to analyze or nifti (MRIcroN):

http://www.cabiatl.com/mricro/mricro/index.html

-isaiah

On Wed, Dec 15, 2010 at 6:03 PM, Xiaodong Tao <[hidden email]> wrote:
Hello Pouria,

You can try the module DicomToNrrdConverter in Slicer3.

For mosaic format, 0020|0032 tag in dicom header may not be the real
image position patient.

Let me know how this works for you.

Xiaodong

On Wed, Dec 15, 2010 at 5:08 PM, pouria mojabi <[hidden email]> wrote:
> Dear Experts,
>
> Hope this email finds you all well.
>
> I am struggling with Image Position(0020, 0032) and Image Orientation(0020,
> 0037) in Dicom images for a while now. I have two conversion tools that spit
> different results when they perform conversion from Dicom to Analyze image.
>
> Debabler from LONI, outputs Analyze image in transverse unflipped format.
> [176 x 256 x 256] and the one that SPM provides gives me coronal unflipped
> with [256 x 256 x 176] being the dimension.
>
> My Dicom's direction cosine is :
> 0.06     0.09     -0.12     0.03     -0.12     -0.99
> and the Image position is:
> -11.2     -123.2 130.29
>
> Does slicer provide a conversion tool for regular Dicoms and Dicom mosaic?
>
> I would really appreciate any advice on what the truth is, or better say,
> which one i should stick with. any pointers on this topic is also highly
> appreciate it. I need to understand the mechanics of such conversions and
> why orientation has a vicarious nature.
>
> Thank you very much indeed
> Pouria
>
>
> _______________________________________________
> 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
>



--
Xiaodong Tao
_______________________________________________
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
To unsubscribe: send email to [hidden email] with unsubscribe as the subject