Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Use 'acq' and 'task' as a suffix for modality name #36

Open
sinhaharsh opened this issue Mar 23, 2023 · 3 comments
Open

Use 'acq' and 'task' as a suffix for modality name #36

sinhaharsh opened this issue Mar 23, 2023 · 3 comments

Comments

@sinhaharsh
Copy link
Collaborator

Problem: Just using datatype (e.g. anat or func) is not sufficient. It leads to erroneous compliance reports.
Why:

  1. A user may use a custom label to distinguish a different set of parameters for acquiring the same modality. This can be highlighted in filename by the label acq.
  2. Similarly, different tasks in fmri may have different set of acquisition parameters

Therefore, it is not quite right to raise alarms for non-compliance, when the changes in parameters are intended,

@sinhaharsh
Copy link
Collaborator Author

But, just acq or task are sufficient?

According to BIDS,

filename is a chain of entity instances and a suffix all separated by underscores and an extension. For instance, file sub-01_task-rest_eeg.edf contains instances of the subject and task entities, the suffix eeg and extension .edf

There are many other entities. See entity table

Should we also consider other entities? I think Yes.

For example, entity dir- should be included to solve #26

Similarly, suffix is also very important. For example, possible suffixes for anat are T1w, T2w, FLAIR, mprage etc.

So what should we do?

The files should be stratified by all entities and the suffix (except for subject - sub and session - ses).

This is because, a common suffix, indicates a group of files. Moreover,

Within each collection, files MUST be distinguished from each other by at least one entity (for example, echo) that corresponds to an altered acquisition parameter (EchoTime) or that defines a component relationship (for example, part)

@sinhaharsh
Copy link
Collaborator Author

If we do this, we may not have to stratify explicitly by echo time for BIDS.

@raamana
Copy link
Contributor

raamana commented Mar 24, 2023

dir- (aka PED) is only required for fmap (epi, m0scan), so never mind about PED, FA and TI for now (as they seem parameters to me), and use the rest as differentiating entities.

prioritize SequenceName (MPRAGE, FLAIR, EPI etc) over the generic high-level Modality description such as (anat, func etc)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants