robertoostenveld/bids-tools

test fails

Opened this issue · 2 comments

schoffelen commented

Hi Robert,
Thanks for your efforts.
I have created a test directory /project/3011020.09/raw/testdir, which currently contains a single subject, according to: sub-2009/ses-meg01/etc (I must admit that at the sub-2009 level there are a few additional files)

I naively tried to run the create_sidecar_files with the -t option as:

./create_sidecar_files -t /project/3011020.09/raw/testdir

and got the following error:

Traceback (most recent call last):
File "./create_sidecar_files", line 274, in
raise NameError('ERROR: type is missing')
NameError: ERROR: type is missing

Dan witte gij dat.

robertoostenveld commented

I encountered it as well and realize that in the standard DCCN data stream and in the reorganize_ctf_dataset script the "meg" directory is not inserted.

it is now

raw/sub-001/ses-meg01/sub-001_ses-meg01_meg.ds

but should be according to BIDS main spec

raw/sub-001/ses-meg01/meg/sub-001_ses-meg01_meg.ds

The same applies to MR, where anat/func/dwi etc is to be used. The difference (in our streamer and my reorganize scripts) is that for MR the number and name of the scan is inserted at that level.

robertoostenveld commented

I wonder whether we should allow for "typ" missing (easy to implement) or whether we should be more strict.

I also wonder whether we (i.e. the TG) should fix this for all data on the repository and project storage. Probably something that @hurngchunlee would not like ...