Trying to load .nii file generated with Nipype

Dear all,

I’m new on Slicer after some work with Nipype. I would like to display the results of my work which is a registration between a T1 and a Scan of the same patient on Slicer. Nipype workflow generates a .nii file. I tried to import it with the Add data function of Slicer and when I press the OK button of the window nothing happens, no message in the bottom box. I looked for research ideas on internet but I found nothing. I’m sorry but I don’t have any information about the import error. I see nothing in the bottom console of Slicer.

Could you help me with research ideas to solve the problem ? Search in the header of .nii ? Specific generation of .nii with Nipype ?

Thanks in advance for your help

Quentin

Is there any error in the application log? If not, then you need to share an example file so that we can investigate the problem.

I just found the log of the error. It is weird that I can display the file with matplotlib in python through Nipype and that Slicer says the file does not exist. Please see below :

vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file /Users/quentinfrancois/Documents/Robeaut�/brain_imaging/results/registrationT1Scan/result.0.nii does not exist.

Algorithm vtkITKArchetypeDiffusionTensorImageReaderFile(0x7fa6150ec7e0) returned failure for request: vtkInformation (0x600001400240)
Debug: Off
Modified Time: 2787208
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0

vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file /Users/quentinfrancois/Documents/Robeaut�/brain_imaging/results/registrationT1Scan/result.0.nii does not exist.

Algorithm vtkITKArchetypeImageSeriesVectorReaderSeries(0x7fa6150e9070) returned failure for request: vtkInformation (0x6000017fce40)
Debug: Off
Modified Time: 2788701
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0

vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file /Users/quentinfrancois/Documents/Robeaut�/brain_imaging/results/registrationT1Scan/result.0.nii does not exist.

Algorithm vtkITKArchetypeImageSeriesScalarReader(0x7fa6150e6c50) returned failure for request: vtkInformation (0x6000017fee00)
Debug: Off
Modified Time: 2789484
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0

ReadData: This is not a nrrd file

ReadData: Cannot read file as a volume of type DiffusionTensorVolume[fullName = /Users/quentinfrancois/Documents/Robeaut�/brain_imaging/results/registrationT1Scan/result.0.nii]
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 /Users/quentinfrancois/Documents/Robeaut�/brain_imaging/results/registrationT1Scan/result.0.nii []
FileNotFoundError

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 = /Users/quentinfrancois/Documents/Robeaut�/brain_imaging/results/registrationT1Scan/result.0.nii]
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 /Users/quentinfrancois/Documents/Robeaut�/brain_imaging/results/registrationT1Scan/result.0.nii []
FileNotFoundError

Quentin FRANCOIS

quentinfrancois0@gmail.com

You need to save the file in a path that does not contain special characters.

Dear Andras,

It was so easy. Sorry for the basic question.

Thanks for your help, it worked directly !

Quentin FRANCOIS

quentinfrancois0@gmail.com

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