general-discussion
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.
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.
Threaded View
Title | Author | Date |
---|---|---|
Ami Tsuchida | Oct 25, 2016 | |
Pierre Bellec | Oct 25, 2016 | |
Ami Tsuchida | Oct 25, 2016 | |
Pierre Bellec | Oct 26, 2016 | |