Issue using Swiss Skull Stripper Module

Hello,

I just started trying out 3D Slicer: currently using version 4.9.0

I thought I entered the correct information into the GUI, but when I went to run it I received the following error:

Swiss Skull Stripper standard error:

Failed to read input atlas label volume.

itk::ImageFileReaderException (0x104a50388)
Location: "unknown" 
File: /Users/kitware/Dashboards/Nightly/Slicer-0-
build/ITKv4/Modules/IO/ImageBase/include/itkImageFileReader.hxx
Line: 143
Description:  Could not create IO object for reading file 
/var/folders/0c/l9qjt85j7ns3j3lctwhs82wc1kd6y7/T/Slicer-dlevitas/CACHI_vtkMRMLLabelMapVolumeNodeB.nrrd

The file doesn't exist. 

Filename = /var/folders/0c/l9qjt85j7ns3j3lctwhs82wc1kd6y7/T/Slicer-
dlevitas/CACHI_vtkMRMLLabelMapVolumeNodeB.nrrd

I already converted my Dicoms using a different program, and my atlas and input files are in NIFTI format; however, I’m unsure if things are failing because the files aren’t in .nrrd format.

Does anyone have any suggestions regarding this issue? Thanks for the help.

Dan

Try to change temporary folder in Application Settings to a simpler one (when your username contain non-ascii characters then the default temporary folder location may not work).

Also, right now we are changing many things in the nightly builds, so for a couple of weeks it may be better to use the stable version (4.8).

Hi Andras,

Thank you for your response. I installed the stable version for Mac OS X (ver 4.8.1), and changed the temporary folder, but I continue to get a similar error:

Swiss Skull Stripper standard error:

Failed to read input atlas label volume.

itk::ImageFileReaderException (0x105ae8938)
Location: "unknown" 
File: /Users/kitware/Dashboards/Package/Slicer-481-
package/ITKv4/Modules/IO/ImageBase/include/itkImageFileReader.hxx
Line: 143
Description:  Could not create IO object for reading file 
/Users/dlevitas/Desktop/3Dslicer/CFJGF_vtkMRMLLabelMapVolumeNodeB.nrrd
The file doesn't exist. 
Filename = /Users/dlevitas/Desktop/3Dslicer/CFJGF_vtkMRMLLabelMapVolumeNodeB.nrrd

It seems that it can’t find the CFJGF_vtkMRMLLabelMapVolumeNodeB.nrrd file, but I’m unsure where this file would be, or how to perform the skull strip without it.

For “Atlas mask volume” you have to select atlasMask volume. Note that the volume only shows up there if it is loaded as “labelmap”. Unfortunately, atlasMask.mha file is not loaded as labelmap by default but in the Add data window you have to check Show options and then check LabelMap.

@Lorensen Could you rename the atlas mask file to atlasImage-label.mha? If a volume’s file name ends with -label then it is loaded as LabelMap by default and it would make it much easier to use the module. Or, even better, extensions can register their own data sets in Sample Data module, so the user could easily go to Sample Data module and download the mask by a single click. See how it is done for Sequences module: https://github.com/SlicerRt/Sequences/tree/master/SequenceSampleData

I was having trouble navigating the GUI, however, I managed to solve my problem by using this in the terminal command line:

/Applications/Slicer.app/Contents/Extensions-26813/SwissSkullStripper/lib/Slicer-4.8/cli-modules/SwissSkullStripper --atlasMRI atlas_with_skull.nii.gz --atlasMask atlas_no_skull_mask.nii.gz input_data.nii.gz output_brain_no_skull.nii.gz output_mask_no_skull.nii.gz

You can also use default atlas by not specifying any atlas image or mask inputs at all.

Hi andras,
I have used skull stripper multiple times. it does do good with sample data. but not with other data.

How can I fix the above problem. it misses the brain portion.

Thank you
Regards,
Saima Safdar

If your images are too different from the default atlas then you can use one of your own typical images and corresponding segmentation as input.

Hi Andras,

I am having the same issue as Saima and I am trying to create a atlas using my own typical images as you said in your last reply. I am a bit stuck, do you have any resources or tutorials that can help with explain this process?

Regards,
James

The atlas is simply a single image and corresponding labelmap. You can choose these images in the atlas section and skull stripping should just work. If not then describe in detail what did you do, what did you expect to happen, and what happened instead.