simtk.org

Hi everyone,

I am segmenting a set of images and want to segment the original images, with no rotation, reflection or interpolation. Turning off the interpolation seems to be working, but the images are still rotated and reflected.

Is there a way to ensure that I am seeing the original scan information in the original orientation? I tried changing the direction of the points on the path, and manually swapping signs on the tangents in the xml files, but no luck so far.

Thank you,
Alex

Hey Alex,

The rotation and reflection are import options? I have not played around with these myself actually. Have you loaded in other software and compared to what you see there?

Hello Alex,

If the .vti was created using the old SimVascular (e.g. all of the data sets included in the Vascular Model Repository), then the image volume is reoriented into RAS space. The Qt GUI is in LPS (the DICOM standard). The only way to avoid the miss labeling is to load in the original DICOM data. Note the signs are different in the R/L, A/P directions (but identical in I/S) which leads to what you are referring to as the reflection if I understand you correctly.

It is possible to use VTK filters to reorient the volume (which was done in the first place), but this is a bit tricky.

There is a potentially bigger issue for MRA data if it's not axially aligned since the VTI can only represent volumes aligned with the coordinate axes. These are called oblique volumes, but I'm not sure if this is done for heart scans.

Nathan

Hi Alex,

If you'd like to work on the original images(DICOM), you can load it by selecting/opening one of the dicom images, you will get the right orientation for the images.

If you want to rotate or reflect an image, you can use the tool "BasicImageProcessing" and select the operation "Flipping" and flip the image across an axis.

Hongzhi