I have some DICOM files which contains different CT reconstructions of temporal bones. Some of the reconstructions use parallel slices which work fine in Slicer, but som use slices which are oriented at different angles around an axis that passes through the cochlea. Similar to the black lines in this image, but for the temporal bone:
In the DICOM browser, I’m getting a list of 144 images:
<MPR Thick Range>
<MPR Thick Range> - imageOrientation 1
<MPR Thick Range> - imageOrientation 2
<MPR Thick Range> - imageOrientation 3
<MPR Thick Range> - imageOrientation 4
<MPR Thick Range> - imageOrientation 144
The DICOM file is generated by a Siemens CT system, and the data is accompanied by a Windows viewer which allows me to easily scroll through the radial slices, but I am not able to get a usable visualization in Slicer of these “radial slices”. When I mark any single image and open, all I’m getting is a thin line in each of the red, yellow and green view fields. By using the “Reformat” module I am able to rotate the image so that I can see more than just a thin line in the red viewer, but I have not been able to find out how to scroll through the images corresponding to different slice orientation angles.
Is it possible to get all the 144 images into Slicer and scroll through them easily?
Slicer is preserving the orientations but it sounds like you want to ignore them, at least for viewing, so maybe try a different converter that ignores orientations and puts the slices into a single nrrd or nifti file. But of course you would lose information that way. Is your goal just to look at them or do you want to do some kind of analysis?
Currently, only 3D image volumes (that have more than 1 slice per time point) are recognized by MultiVolumeImporter module’s DICOM importer. You need to tune
MultiVolumeImporterPlugin.py file to change its logic to accept single-slice volumes.
Why don’t you just use regular Cartesian reconstruction? What would you like to do with these images slices?
have you looked at the reformat module?
The adjustments needed in the reformat module to make the whole slice visible are quite time consuming even for a single slice, so I will not be able to to that on all the slices.
It would be better to be able to ignore the orientations, so that the slices could be inspected easily at least. At first I will just inspect the images, but would also be nice if it was possible to make some distance calculations within each slice.
I have the same CT data available also using a Cartesian reconstruction, but those radial planes were ment to make it easy to inspect the angular dependency of the placement of a cochlear electrode inside the cochlea, so it would be nice to be able to scroll through them.
The DICOM viewer that accompanies the data export from the Siemens system simply shows all the slices, but it also includes text showing the angle of each plane. I’m working mostly on Linux, but perhaps I could find some other DICOM viewer software that will simply display the slices on after the other an not try to embed anything in 3d space.
You can enable in Application settings (DICOM/Allow subseries loading by time) to show each slice as a separate loadable in DICOM module (when “Advanced” checkbox is checked). You can easily switch between which volume is shown by clicking eye icon of a data set in Data module / Subject hierarchy tab.
You can show see the whole slice in a slice viewer if you click “Rotate to volume plane” button.
If you share an example data set then we may be able to tune the DICOM import script to be able to load all the frames at once, as a volume sequence.
Thanks, that’s quite nice. So what remains is to be able to do this for the whole series, as you point out. Unfortunately I cannot share any of the data due to patient privacy concerns. I’ll investigate if we have some non-patient data with a similar reconstruction, then I’ll be able to share it. Thanks! I also found out that using something called Ginkgo CADx which also works on Linux, I was able to quickly scroll through the those type of slices, but it would be neat to do it in Slicer.