[Neuroimaging] first dimension too large

[Karla Kort]

Hi,

I am trying to write to a new Nifti file in python, but I get this error when running the script from the commandline: 'UserWarning: Using large vector Freesurfer hack; header will not be compatible with SPM or FSL' And this file does not work. When I run the script in jupyter notebook it doesn't give an error, but the file still still doesn't work and seems empty.  I read online that this is because the first dimension is too large, the dimensions of my data are (498511, 1, 1). So I guess that really is the problem, but I could not find any way to work around this. Is there a way? I do really need the complete file.
Also, is there a way to just replace the data part in a nifti file? I noticed that .set_fdata() is not an existing command.

Kind regards,
Karla
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