[fli-iam#1864] Add NIRS type BIDS

[youennmerel]

NIRS BIDS files can now be imported into Shanoir

Specs : https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/11-near-infrared-spectroscopy.html

How to test :

• Import NIRS modality BIDS into Shanoir through the BIDS import
• Check the created examinations/acquisitions/datasets

Data samples :
https://osf.io/juxy8
https://github.com/bids-standard/bids-examples#nirs-datasets

[michaelkain]

Hi, I think we could extend the import description to add NIRS [anat/func/dwi/eeg/ieeg/pet/..] on the web page to show, what modality we support.

[michaelkain]

Hi, I think we might have to verify, if today's acquisition equipment fits to NIRS. So, when we create an unknown equipment, is it possible for somebody to enter the equipment info for NIRS OR do we risk to create unknown-unknown equipments? I know for MR, CT (not yet in BIDS) and PT we are fine, but I think there might be a gap with NIRS?

[youennmerel]

@michaelkain added 'Nirs' as BIDS data type in study card

[michaelkain]

Very good! Concering my comment on the equipment: I am right, that it remains empty for NIRS in the ds_acquisition? What is by the way totally fine for me. I just wanted to avoid dangling "unknown" equipments.

[youennmerel]

Added manufacturer model modality type 'Nirs'

[youennmerel]

Very good! Concering my comment on the equipment: I am right, that it remains empty for NIRS in the ds_acquisition? What is by the way totally fine for me. I just wanted to avoid dangling "unknown" equipments.

It will remain empty if none are found. However we now can also create 'Nirs' equipment in Shanoir.

[youennmerel]

Hi @michaelkain,

Should be OK now !

[michaelkain]

Hi Youenn, thank you for your corrections. I downloaded one of the big NIRS examples above and did some tests, that showed some strange outputs:

1. Good point: the import finishes with success: OK
2. The import message in jobs has an error: [null (n°1)] Successfully created datasets for subject [DemoStudy_06] in examination [1] : the study name should not be null in the jobs message
3. Solr download, as BIDS dataset: my subject folder sub-06 contains 34 files in my original BIDS structure: when I download all datasets imported, I have only 5 files, what should not be the case. The question is, how do we consider the datasets generated from BIDS. And when I download I have a full failures.txt and the file names in my zip file contain null_null values.
4. the produced BIDS tree looks quite correct (study details), but contains a sub-2-DemoStudy06_scans.tsv file in Shanoir with 35 lines, but the original contains 36 lines on my disk (to correct)
5. how do you map the files into the datasets in Shanoir? do you interpret the scans.tsv file, that contains 36 fnirs files?
6. the other files in the tree are complete, and have the same naming

[michaelkain]

Hi, sorry, there is another issue:

the file names are wrong: they contain two times the subject
so you have to remove the old "sub-06" from the file name, as the subject has been imported into shanoir

[michaelkain]

more issues:

• the link to the created examination in shanoir is broken, from the created datasets
• same for the created dataset acquisition
• and no equipment is linked, neither created from the information of the BIDS structure

[michaelkain]

Hi @youennmerel, please see my comments. Thank you!

[youennmerel]

Hi @michaelkain,

I took your comments into account, except for (as discussed in daily) :

• Solr BIDS download : should be dealt with in another issue
• scans.tsv content : in your example, the imported scans.tsv is incorrect, the generated one is.

[michaelkain]

Hi @youennmerel, thank you! The 2 issues above are now fixed. I found two new ones, see my screenshots. I think with multiple sessions you just have to remove the trailing "-" from "ses-1-". I am wondering, as we have the acquisition time in the scans.tsv, if we could not use this as exam date, without time stamp maybe?

[michaelkain]

and it is strange, that in the Shanoir tree, the dataset do not have the same name "subject name" contained as in the BIDS tree, but maybe this is normal...?

and I think the subject_name BIDS-test06 should be the same everywhere?

[michaelkain]

Hi @youennmerel, I hope you had a good start into your day. For the <label>s, see BIDS spec:
label - An alphanumeric value, possibly prefixed with arbitrary number of 0s for consistent indentation, for example, it is rest in task-rest following task- specification. Note that labels MUST not collide when casing is ignored (see Case collision intolerance).
sub

Full name: Subject
Format: sub-<label>
Definition: A person or animal participating in the study.
ses

Full name: Session
Format: ses-<label>

[youennmerel]

Hi @michaelkain,

• Fixed label : now remove non-alphanumeric characters in BIDS tree
• Fixed acq_time parsing : now create examination with acq_time date

[michaelkain]

Nice job @youennmerel !!! Much better looking BIDS tree now, thank you!!!