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Maniphest T19394

fsl import failed
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Description

Trying to read nifti diffusion data.
Renamed data.nii.gz into data.fslgz
bvecs -> data.fslgz.bvecs
bvals -> data.fslgz.bvals

When trying to open get the following error

Error reading files

Exception occured when reading file ~~~\MITK_diffusion\data.fsl:
..\..\..\..\..\tommy\MITK\Modules\DiffusionImaging\DiffusionIO\mitkNrrdDiffusionImageReader.cpp:408:
..\..\..\..\..\ITK-src\Modules\IO\NIFTI\src\itkNiftiImageIO.cxx:937:
itk::ERROR: NiftiImageIO(0000000005752EE0): temp_dwi.nii.gz is not recognized as a NIFTI file

tried with non uncompressed files
data.nii -> data.fsl
bvecs -> data.fsl.bvecs
bvals -> data.fsl.bvals
the same outcome

best wishes

Event Timeline

kraskov added projects: MITK, Bugzilla.Oct 26 2015, 12:45 AM
• hering added a subscriber: • hering.Oct 26 2015, 11:34 AM

From the error log, the reading fails already in the itkNiftiImageIO class, hence I strongly suspect the data itself is somehow corrupted.

If this is so, the same error should occur when the data is loaded not as a diffusion-weighted image (copy the .nii.gz data to a separate directory without the .bvecs and .bcals files and use the File>Open dialog).

Or if possible, could you provide the data for testing? Can FSL itself read the data?

kraskov added a subscriber: kraskov.Oct 26 2015, 4:40 PM

Dear Jan,

I checked the file and it is fine (I can open it in MITK as an image, I presume it opens the first volume of 4d file, and I can open it with fsl and mricro).

the file is a data set from human connectome project

I can upload it or you can get it from there (id 100307)

best wishes

kraskov added a comment.Oct 30 2015, 12:27 AM

Dear Jan, is there any progress on this issue.
I just with another diffusion file which is loadable in any other software I tried and I still get the same error.

Happy to give you link to download the file.

Best wishes

kraskov added a comment.Nov 5 2015, 10:52 PM

Dear All,

problem solved. It turned out to be permission problem. The error message is identical on Windows or Linux.

While opening diffusion files, FSL import creates a temporary file and probably does it in the directory the application is started from.

If MITK diffusion executed under Administrator rights FSL import does not fail.
Or one can just run it in your home directory (or any other directory you have permission to write).

cheers

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