Bids filter troubleshooting

1

I am trying to filters bids dataset , below is my json file , somehow it doesnt pick up the corresponding t2w json along with nii.gz.

input file is
I am new to bids-filter.

{
        "t2w": {"datatype": "anat","suffix":"T2w", "run":"2","session":"V02","SeriesDescription": "anat-t2w","ProtocolName": "anat-t2w","extension": ["nii.gz", "json"]}

}
2

Hi @mbilas, and welcome to neurostars!

Those don’t go in the filter. You can see an example filter here: FAQ - Frequently Asked Questions — fmriprep version documentation

It would also help to see the tree output on your subject’s data to see what a filename looks like.

Best,
Steven

3

Thank you Steven ! see the attachment for tree structure. My bids filter (above) should aim in only filtering run-2 T2w json and nii.gz file.

image
image776×382 55.5 KB

4

Hi @mbilas,

Using a null acquisition in the filter should help only get those last files.

Best,
Steven

5

No change in output still only nii.gz file is filtered even after acquisition is set to null.

Regards
Monalisa

6

It would help to provide all of the information usually requested for in the Software Support post template. As well as the updated BIDS filter file. Also, what exactly do you mean by “only nii.gz file is filtered”?

Best,
Steven