general-discussion > RE: failed time_filter
Oct 25, 2016  05:10 PM | Pierre Bellec
RE: failed time_filter
Hi Ami,

Thanks for trying out the docker image! 

So the error message says the Nyquist frequency here is 0 Hz. That is not good :)

Very likely a corrupt nifti header, with TR set to zero second. Would you mind sharing an example (raw) fmri file via email/drpobox? 

You can also check yourself:

```
[hdr,vol] = niak_read_vol('file.nii');
hdr.info.tr
```

If that's the problem, and you know the TR, you can fix the files manually (or in a for loop if there are a lot...):
'''
[hdr,vol] = niak_read_vol('file.nii');
hdr.info.tr = 2; % Example TR = 2 s
hdr.file_name = 'file_correct_tr.nii';
niak_write_vol(hdr,vol);
'''

The new file 'file_correct_tr.nii' will have the correct TR. Also note that niak can handle .nii.gz files to save space. 

Let me know if that helps. Best,

Pierre

PS: if you have processed these data in other software and did not manually specify TR, you may want to check that filtering was properly done. It may have produced non-sensical results without crashing.

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TitleAuthorDate
Ami Tsuchida Oct 25, 2016
RE: failed time_filter
Pierre Bellec Oct 25, 2016
Ami Tsuchida Oct 25, 2016
Pierre Bellec Oct 26, 2016