Thank you for all your suggestions.
Below is an example of one of the scenes I have tried to convert manually. I can load the XML file into Slicer 4.8 without errors but the image is not loaded. However, in the Data module, the node “brain1st” is created with the correct image spacing. Are there any obvious mistakes in the MRML file, or could it be that Slicer does not recognise the file format of the volume data? There are 60 slices named brain1st.001, brain1st.002 etc.
Original MRML v1.0 (Slicer 1 or 2):
MRML V1.0
Volume (
name brain1st
labelMap 1
filePrefix brain1st
headerSize 0
imageRange 1 60
spacing 0.9375 0.9375 2.5
rasToIjkMatrix 0 1.06667 0 122.773 -1.06667 0 -0 140.8 0 -0 0.4 23.14 -0 0 -0 1
rasToVtkMatrix -0 1.06667 -0 122.773 1.06667 -0 0 115.2 -0 0 0.4 23.14 0 -0 0 1
options slicer interpolate 0 lutID 6
)
Converted MRML v2.0 (Slicer 4):
<?xml version="1.0" standalone="no"?>
<!DOCTYPE MRML SYSTEM "mrml20.dtd">
<MRML>
<Volume
name="brain1st"
labelMap="1"
filePrefix="brain1st"
headerSize="0"
imageRange="1 60"
spacing="0.9375 0.9375 2.5"
rasToIjkMatrix="0 1.06667 0 122.773 -1.06667 0 -0 140.8 0 -0 0.4 23.14 -0 0 -0 1"
rasToVtkMatrix="-0 1.06667 -0 122.773 1.06667 -0 0 115.2 -0 0 0.4 23.14 0 -0 0 1"
interpolate="no">
<!-- Not used: -->
<!-- options slicer interpolate 0 lutID 6 -->
</Volume>
</MRML>
When I load the new MRML file in Slicer 4.8 I get the following output in the terminal:
"MRML Scene" Reader has successfully read the file ".../brain1st/brain1st.xml.mrml" "[0.34s]"
Input port 0 of algorithm vtkImageMapToColors(0x2ed5040) has 0 connections but is not optional.
No scalar values found for texture input!
If I try to load the image data alone (without the MRML scene file) I get the following error:
ReadData: This is not a nrrd file
ReadData: Failed to instantiate a file reader
ReadData: Cannot read file as a volume of type Volume[fullName = .../brain1st/brain1st.001]
Number of files listed in the node = 0.
File reader says it was able to read 0 files.
File reader used the archetype file name of .../brain1st/brain1st.001 []
ITK exception info: error in unknown
Could not create IO object for reading file .../brain1st/brain1st.001
Tried to create one of the following:
NiftiImageIO
NrrdImageIO
GiplImageIO
JPEGImageIO
GDCMImageIO
BMPImageIO
LSMImageIO
PNGImageIO
TIFFImageIO
VTKImageIO
StimulateImageIO
BioRadImageIO
MetaImageIO
MRCImageIO
MINCImageIO
MGHImageIO
MRMLIDImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
Is there a way to set the file type without changing the file extension? If not with the GUI, perhaps using Python?
Isaiah, I did find some similar code in my search so I got the Slicer2 source from Steve’s github page but ran into some trouble trying to compile it. I fixed a lot of the errors but eventually gave up hoping to find a better way to import the files into the new Slicer. Did you compile Slicer2 from source or did you use a precompiled binary for Windows?
Steve, I tried to load the scene and image in Slicer 3.6.3 but this did not work either. I will try again to compile Slicer 2. Would you expect there to be any problems building Slicer 2 or 3 on Debian 9 (stretch)?