simtk.org

Hi,

I have been trying to import a DICOM stack but am only able to import what seems like a single slice or none at all.

The error below has also been appearing for almost every stack. Is this an error that can be neglected?

[17.509] Reader 4 (Image Position by Acquisition) suggests 24 3D blocks
#17.638# ERROR: Reader 5 (2013 default sorting for 3D+t) threw exception during file analysis, ignoring this reader. Exception: Invalid tag values when constructing tilt information from origin1 '', origin2 '', and orientation ''
#17.773# ERROR: Reader 6 (IPP 3D+t) threw exception during file analysis, ignoring this reader. Exception: Invalid tag values when constructing tilt information from origin1 '', origin2 '', and orientation ''
#18.534# ERROR: Reader 7 (3D+t by AcquisitionNumber) threw exception during file analysis, ignoring this reader. Exception: Invalid tag values when constructing tilt information from origin1 '', origin2 '', and orientation ''
#18.676# ERROR: Reader 8 (3D+t by TriggerTime) threw exception during file analysis, ignoring this reader. Exception: Invalid tag values when constructing tilt information from origin1 '', origin2 '', and orientation ''
Thanks,
Shion

You can try to use VolView https://www.kitware.com/volview/ to load a DICOM stack and save it as a vti file. Then load the vti file into SimVascular instead.

Hi Shion,

Problems reading in DICOM are often caused by having multiple sequences in the same folder. The DICOM reader tries to stack the images into a 3D volume but this fails when you have images at the same location.

Cheers,
Dave

Hi,

I've been trying to use VolView but it seems the software is outdated on Mac OS. When VolView was suggested, did you mean for it to be used on Windows/Linux?

Best,
Shion

Hi Shion,

VolView is way out of date, crashes on MacOS.

I've written a Python script that converts DICOM to a VTK .vtk image. This file can then be read in by SV. Have a look here https://github.com/ktbolt/cardiovascula ... vti/python. I tested this on a Mac.

Cheers,
Dave

Hi Dave,

Thanks! I will give this a try.

Best,
Shion

Hello Dave,

How can I go about running the source code you posted? I am new to coding and I'm unsure of how to run source code posted by others on GitHub.

Thanks,
Joanne

Hi Joanne,

You can view the Python script here (https://github.com/ktbolt/cardiovascula ... -to-vtk.py) and then select the Raw button located on the panel the code is displayed in. This will display the script in the web browser which you can then save to a file using the File/Save As menu option.

You can then run the script as described in the README file.

Cheers,
Dave