I added video tutorials on how to register and fuse and segment cochlea multi-modal images using our VisSim Tools extension that uses elastix toolbox as well. The source code can be found here.
Sample cochlea datasets are also shared and can be downloaded using “Data Store”
module.
This is still a beta version and more enhancement will be added to both source code and videos.
It does appear in the extension manager for me with the current nightly build on Linux (4.11.0-2018-10-23 r27518), but it doesn’t seem to work. I’m getting the following error messsage in the terminal window where I start Slicer:
$ slicer
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/torquil/.config/NA-MIC/Extensions-27518/SlicerCochlea/lib/Slicer-4.11/qt-scripted-modules/CochleaReg.py", line 24, in <module>
import Tkinter, tkFileDialog
ImportError: No module named Tkinter
loadSourceAsModule - Failed to load file "/home/torquil/.config/NA-MIC/Extensions-27518/SlicerCochlea/lib/Slicer-4.11/qt-scripted-modules/CochleaReg.py" as module "CochleaReg" !
Fail to instantiate module "CochleaReg"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/torquil/.config/NA-MIC/Extensions-27518/SlicerCochlea/lib/Slicer-4.11/qt-scripted-modules/CochleaSeg.py", line 25, in <module>
import Tkinter, tkFileDialog
ImportError: No module named Tkinter
loadSourceAsModule - Failed to load file "/home/torquil/.config/NA-MIC/Extensions-27518/SlicerCochlea/lib/Slicer-4.11/qt-scripted-modules/CochleaSeg.py" as module "CochleaSeg" !
Fail to instantiate module "CochleaSeg"
Ok, I installed the latest Slicer 3D nightly for Linux, and now I’m getting this error on the terminal after picking a point in the middle of the cochlea in a CT image, and then clicking on “Run”:
Switch to module: "CochleaSeg"
=======================================================
Automatic Cochlea Image Segmentation
=======================================================
Default Settings:
VisSimTools folder: /home/torquil/VisSimTools
Output folder : /home/torquil/VisSimTools/outputs
Parameter file: /home/torquil/VisSimTools/pars/parCochSeg.txt
Cropping Length: 10
elastix binaries are found in /home/torquil/VisSimTools/sw/elastix-4.9.0/bin/elastix
Other files are found !
Traceback (most recent call last):
File "/home/torquil/.config/NA-MIC/Extensions-27526/SlicerCochlea/lib/Slicer-4.11/qt-scripted-modules/CochleaSeg.py", line 746, in updateLengthBtnClick
ptsRASNode = self.markupsNode
AttributeError: CochleaSegWidget instance has no attribute 'markupsNode'
..... getting cochlea location in the input image
..... cochlea location RAS: [38.186453904880466, 170.83668361478453, 225.1563957681987, 1.0]
..... cochlea location in the fixed image set to: [85, 301, 299]
removing old output folder!
Traceback (most recent call last):
File "/home/torquil/.config/NA-MIC/Extensions-27526/SlicerCochlea/lib/Slicer-4.11/qt-scripted-modules/CochleaSeg.py", line 465, in runBtnClick
self.inputPath = self.inputNode.GetStorageNode().GetFileName()
AttributeError: 'NoneType' object has no attribute 'GetFileName'
Within Slicer, the “Run”-button turned red and says “…please wait”, but nothing is happening and the timer is not counting.
Thanks for testing.
I could not reproduce the problem. Does the cochlea registration module work?
Please try these steps:
save your cochlea image in your home folder as nrrd format. Sometimes elastix does not recognize filenames with special characters or spaces, e.g. use this filename. /home/torquil/img.nrrd
Do you really need OpenCL? Could you include runtime libraries in the extension instead of asking the user to manually download and install development packages? Many users are not comfortable with installing additional software tools.
If there is no chance for a better solution then at least the extension should detect if some OpenCL component is missing and display a meaningful error message - with an explanation and download link.
Do you really need OpenCL? Could you include runtime libraries in the extension instead of asking the user to manually download and install development packages?
Thanks for your comment. You are right. I used my elastix binaries as a temporary solution as I am planning to use SlicerElastix instead.
I have a problem with the cochlea segmentation module.
This modul create always the same cochlea that is not consist with the real image. I used Slicer 4.10.0 (on the latest version 4.11. this extension not work, always drop an error: 2 arguments expected but 4 were given)
The modul segment this random cochlea also, when I put the markups anywhere on the image.
What is the problem? I tried what happened if I check the right side box.
Do you see any errors in the application log?
If you don’t get an answer here within a couple of days then you can submit a bug report to the extension’s github repository.