DICOM stack imported as one image

[Shion Matsumoto]

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 ''

one_slice.png (120.38 KiB) Viewed 410 times

Thanks,
Shion

[Weiguang Yang]

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.

[David Parker]

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

[Shion Matsumoto]

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I've been trying to use VolView but it seems the software is outdated on Mac OS.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

[David Parker]

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VolView is way out of date, crashes on MacOS.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

[Shion Matsumoto]

Hi Dave,

Thanks! I will give this a try.

Best,
Shion

[Joanne Sarsam]

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

[David Parker]

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