Not able to load Freesurfer Model (lh.pial) on Slicer 5.8.1

Development
1

I’m trying to load a FreeSurfer model (lh.pial) programmatically through a scripted module but I’m not achieving it.

I’ve tried:

fsImporterLogic = slicer.util.getModuleLogic('FreeSurferImporter')
volumeNode = fsImporterLogic.LoadFreeSurferVolume(file_path)

where file_path is the path to one of the files I want to open, and got the following error:

vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open /Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial. ITK exception info: error in unknown:  Could not create IO object for reading file /Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial
[VTK]   Tried to create one of the following:
[VTK]     BMPImageIO
[VTK]     BioRadImageIO
[VTK]     DCMTKImageIO
[VTK]     GDCMImageIO
[VTK]     GiplImageIO
[VTK]     JPEGImageIO
[VTK]     LSMImageIO
[VTK]     MGHImageIO
[VTK]     MINCImageIO
[VTK]     MRCImageIO
[VTK]     MetaImageIO
[VTK]     NiftiImageIO
[VTK]     NrrdImageIO
[VTK]     PNGImageIO
[VTK]     ScancoImageIO
[VTK]     StimulateImageIO
[VTK]     TIFFImageIO
[VTK]     VTKImageIO
[VTK]     MRMLIDImageIO
[VTK]   You probably failed to set a file suffix, or
[VTK]     set the suffix to an unsupported type.
[VTK] Algorithm vtkITKArchetypeImageSeriesScalarReader (0x7f8fc479ae80) returned failure for request: vtkInformation (0x60001155aa00)
[VTK]   Debug: Off
[VTK]   Modified Time: 5320081
[VTK]   Reference Count: 1
[VTK]   Registered Events: (none)
[VTK]   Request: REQUEST_INFORMATION
[VTK]   ALGORITHM_AFTER_FORWARD: 1
[VTK]   FORWARD_DIRECTION: 0
[VTK] vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Reading of file '/Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial' failed: FileFormatError Number of files listed in the node is 0. File reader says it was able to read 0 files. File reader used the archetype file name of '/Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial' (first filename: '')
[VTK] vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Reading of file '/Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial' failed: FileFormatError Number of files listed in the node is 0. File reader says it was able to read 0 files. File reader used the archetype file name of '/Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial' (first filename: '')
[VTK] vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Cannot read '/Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial' file as a volume of type 'Volume'. Details: FileFormatError.
[VTK] vtkMRMLStorageNode::ReadData: Failed to read node lh (vtkMRMLScalarVolumeNode5) from filename='/Users/justo/Library/CloudStorage/GoogleDrive-justo.montoya@upf.edu/Mi unidad/SLICER/test_raw/fsfolder/surf/lh.pial'

I’ve also tried other options like:
modelNode = slicer.util.loadModel(file_path)

But it’s not working either. How can I open this FreeSurfer model programmatically?

Thanks in advance! :slight_smile:

2

The method you tried is for loading images. You can load models (in freesurfer terminology overlays) using LoadFreeSurferScalarOverlay.

3

Thanks.

What is an example usage of LoadFreeSurferScalarOverlay()?

I’ve seen that the logic is defined here SlicerFreeSurfer/FreeSurferImporter/Logic/vtkSlicerFreeSurferImporterLogic.h at master · PerkLab/SlicerFreeSurfer · GitHub but I can’t understand how to apply it to my situation.

4

I misspoke above, Slicer models correspond to freesurfer surfaces (*h.white, *h.pial, *h.inflated, *h.sphere, h.sphere.reg, h.orig files), and Slicer scalar arrays correspond to freesurfer overlays (.area, .curv, *.sulc, *.W files).

Surface reading was reworked about 1-2 years ago to use nibabel and is now implemented in a separate logic. You can use it as it is shown in this test:

slicer.util.loadNodeFromFile() would work if the NiBabelModelIO registered itself as a reader plugin. It would be nice if you could implement it (you would add a NiBabelModelIOFileReader class to the NiBabelModelIO.py and implement a few methods - similarly to this). But if you don’t have the time then you can simply use the NiBabelModelIO module logic directly.