# Trying to load .nii file generated with Nipype

**URL:** <https://discourse.slicer.org/t/trying-to-load-nii-file-generated-with-nipype/6611>\
**Category:** Support\
**Created:** [April 26, 2019, 2:25am UTC](https://discourse.slicer.org/t/trying-to-load-nii-file-generated-with-nipype/6611 "2019-04-26T02:25:34Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![quentinfrancois0](https://avatars.discourse-cdn.com/v4/letter/q/a9adbd/32.png) [@quentinfrancois0](https://discourse.slicer.org/u/quentinfrancois0)\
**Post date:** [April 26, 2019, 2:25am UTC](https://discourse.slicer.org/t/trying-to-load-nii-file-generated-with-nipype/6611/1 "2019-04-26T02:25:34Z")

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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

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [April 26, 2019, 12:56pm UTC](https://discourse.slicer.org/t/trying-to-load-nii-file-generated-with-nipype/6611/2 "2019-04-26T12:56:51Z")

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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.

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**Author:** ![quentinfrancois0](https://avatars.discourse-cdn.com/v4/letter/q/a9adbd/32.png) [@quentinfrancois0](https://discourse.slicer.org/u/quentinfrancois0)\
**Post date:** [April 26, 2019, 2:44pm UTC](https://discourse.slicer.org/t/trying-to-load-nii-file-generated-with-nipype/6611/3 "2019-04-26T14:44:15Z")

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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](mailto:quentinfrancois0@gmail.com)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [April 26, 2019, 3:15pm UTC](https://discourse.slicer.org/t/trying-to-load-nii-file-generated-with-nipype/6611/4 "2019-04-26T15:15:24Z")

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

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**Author:** ![quentinfrancois0](https://avatars.discourse-cdn.com/v4/letter/q/a9adbd/32.png) [@quentinfrancois0](https://discourse.slicer.org/u/quentinfrancois0)\
**Post date:** [May 2, 2019, 3:34pm UTC](https://discourse.slicer.org/t/trying-to-load-nii-file-generated-with-nipype/6611/5 "2019-05-02T15:34:18Z")

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Dear Andras,

It was so easy. Sorry for the basic question.

Thanks for your help, it worked directly !

Quentin FRANCOIS

[quentinfrancois0@gmail.com](mailto:quentinfrancois0@gmail.com)