MITK vs. Slicer: model and dicom images do not overlay

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MITK vs. Slicer: model and dicom images do not overlay

Wang, Anqi

Hi,

 

I used MITK to segment structures in MRI volumes (dicom). Then I generated .stl files from the segmentations using the built in MITK option “create polygon model”. When I use MITK to view the volumes and the .stl files, they overlap neatly. However, if I open exactly the same dicom series in Slicer and add the same .stl files as models, they have what seems like a rotation of 180 degrees around a central point and an offset and clearly do not overlap at all (screenshots attached). Does anyone know the reason for this?

 

Best regards,

 

Anqi


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volum and stl in mitk.png (161K) Download Attachment
volum and stl in slicer.png (58K) Download Attachment
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Re: MITK vs. Slicer: model and dicom images do not overlay

Tamas Ungi-2

Hi Anqi,

 

One of your data (either the volume or the surface) is read into Slicer in the LPS coordinate system, and the other in RAS. Create a new transform, name it LpsToRas and set "IS" under "Rotation" to 180 degrees. Apply this transform on one of your data, and they will match.

 

On the long run, you should use file formats that are correctly read in Slicer too. As far as I remember this is an ITK issue, so Slicer developers cannot really fix it. Are there different file format options when saving an image in MITK?

 

Hope this helps,

Tamas

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Wang, Anqi
Sent: Tuesday, December 02, 2014 12:06 PM
To: [hidden email]
Subject: [slicer-users] MITK vs. Slicer: model and dicom images do not overlay

 

Hi,

 

I used MITK to segment structures in MRI volumes (dicom). Then I generated .stl files from the segmentations using the built in MITK option “create polygon model”. When I use MITK to view the volumes and the .stl files, they overlap neatly. However, if I open exactly the same dicom series in Slicer and add the same .stl files as models, they have what seems like a rotation of 180 degrees around a central point and an offset and clearly do not overlap at all (screenshots attached). Does anyone know the reason for this?

 

Best regards,

 

Anqi


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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: MITK vs. Slicer: model and dicom images do not overlay

Andras Lasso-2

STL cannot store coordinate system or unit, so applications can only make assumptions. Slicer assumes RAS, MITK assumes LPS, that’s why you have the misalignment and the steps that Tamas described can convert between the two.

 

See also:

http://www.slicer.org/slicerWiki/index.php?title=Documentation/Nightly/FAQ#I_used_some_other_software_to_create_.stl_file_and_when_I_open_it_in_Slicer_it_appears_180deg_rotated_.2F_at_incorrect_position

No VTK-supported mesh format specify coordinate system. A solution could be to make the medical image computing community agree in a common assumption or add some custom fields to the mesh files (e.g., we could put some special string into STL file comment field that would specify the coordinate system).

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Tamas Ungi
Sent: Tuesday, December 02, 2014 1:11 PM
To: Wang, Anqi; [hidden email]
Subject: Re: [slicer-users] MITK vs. Slicer: model and dicom images do not overlay

 

Hi Anqi,

 

One of your data (either the volume or the surface) is read into Slicer in the LPS coordinate system, and the other in RAS. Create a new transform, name it LpsToRas and set "IS" under "Rotation" to 180 degrees. Apply this transform on one of your data, and they will match.

 

On the long run, you should use file formats that are correctly read in Slicer too. As far as I remember this is an ITK issue, so Slicer developers cannot really fix it. Are there different file format options when saving an image in MITK?

 

Hope this helps,

Tamas

 

 

From: [hidden email] [[hidden email]] On Behalf Of Wang, Anqi
Sent: Tuesday, December 02, 2014 12:06 PM
To: [hidden email]
Subject: [slicer-users] MITK vs. Slicer: model and dicom images do not overlay

 

Hi,

 

I used MITK to segment structures in MRI volumes (dicom). Then I generated .stl files from the segmentations using the built in MITK option “create polygon model”. When I use MITK to view the volumes and the .stl files, they overlap neatly. However, if I open exactly the same dicom series in Slicer and add the same .stl files as models, they have what seems like a rotation of 180 degrees around a central point and an offset and clearly do not overlap at all (screenshots attached). Does anyone know the reason for this?

 

Best regards,

 

Anqi


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.