Re: [mitk-users] Image orientation flip on segmentation (Siemens 1.5T MRI imaging data)

[Goch, C. J. <c....@Dk...>]

Further discussion will take place in:
https://phabricator.mitk.org/T19882

Thank you Joost for opening a task.

Best,
Caspar

Von: Jo...@gm... [mailto:Jo...@gm...]
Gesendet: Donnerstag, 18. August 2016 09:01
An: mit...@li...
Betreff: [mitk-users] Image orientation flip on segmentation (Siemens 1.5T MRI imaging data)

Hi everybody,

thanks for MITK, which already proves it is a great tool!We are evaluating to employ it in a MRI project involving a lot of segmentation. While the general workflow seems good (segmentation in MITK using its fantastic 3D interpolation capabilities, then exporting .nrrd files for further analysis e.g. in Slicer), we face a minor (is this minor?) problem regarding data loading and segmentation:

Initially, loading the DICOM series from a local directory works and gives us correct orientation (meaning axial, coronal, sagittal) in the viewer. But upon starting the segmentation, the orientations get flipped. This happens when I create a new segmentation, after entering its name. Now, the window named "axial" shows a coronal reconstruction, while "coronal" shows the axial images and "Sagittal" gives a prone view head left.

A "Reinit" on the image series does not help, while a "Global Reinit" restores correct image orientation, but necessitates a reinit on the segmentation, which again flips the images as noted above.

I figure this might be related to http://mitk-users.narkive.com/SvdIsLSz/question-reinit-image-flip<https://deref-gmx.net/mail/client/ND4MJBlkyms/dereferrer/?redirectUrl=http%3A%2F%2Fmitk-users.narkive.com%2FSvdIsLSz%2Fquestion-reinit-image-flip>, but the related bugs show as fixed. We're using MITK Workbench 16.03, are those fixes included?

Imaging data comes from a clinical MRI scanner (Siemens Aera 1.5 T), the sequence is a T1 Dixon 3D sequence. Anonymized dicom imaging data can be provided.

Thanks a lot for any help,

Joost

PS: I already tried to do my share and compile the GIT version as of yesterday. Though the compilation succeeded after several hours, I did not get a successfull package installation on OpenSuse (Workbench starts up, but the plugins are not registered).