Question Regarding Sequence Names

[dlevitas]

Hello,

Our imaging center is beginning to convert all our study DICOMS into BIDS format, and we are planning to use the ReproIn/heurdiconv workflows to accomplish this. I've been going over the provided walkthrough and source code, but have two lingering questions I wanted to clarify.

1). Our scanner collects three localizer DICOMS at the beginning of each protocol; can "localizer" be the seqtype label? In the code I see an option "_ses-localizer"; however, we're not planning on specifying session, so can a localizer scan just be listed as "localizer"?

2). Our sequence names normally have additional information appended at the end (i.e. _mb4_870vols or _MPRANGE_0.8mm). It seems like this information could be included in the _custom label; however, is it better to not include this in the sequence names, since this information is in the metadata anyway?

Thanks for the assistance.

Dan

[yarikoptic]

1) "scouts" (which I guess the localizers are) aren't covered by BIDS AFAIK. in reproin heuristic we do not convert them into BIDS, but do retain their dicoms under sourcedata/, see e.g. http://datasets.datalad.org/?dir=/dbic/QA/sourcedata/sub-qa/ses-20180910/anat

_ses-* is completely optional and just used to describe session where needed. We call them anat-scout. localizer is not defined in ReproIn. But if you already have them, we can figure out a workaround

2) up to you to decide. When ppl really want those to be present, we just list them within _acq- field

[dlevitas]

Thanks @yarikoptic for your response. To clarify:

1). As far as I'm aware, we have two separate localizer protocols: AAHead_Scout and a normal localizer, which have different names in our system. It seems that the Scout localizers could simply be named anat-scout; however, would this also be appropriate for the other localizer protocol? We currently haven't collected any data with the new sequence names, but I'm trying to make sure the names can be recognized by the reproin heuristic.

2). I'll have to see what our MRI physicist thinks about this, but for now we'll plan to keep the sequence names short (i.e. not use the optional labels) for now. If however we choose to add more information to the sequence names, would something like anat-T1w_acq-MPRANGE-0.8mm or func_task-nback_run-01_acq-mb4-2mm be acceptable?

[yarikoptic]

1). If that localizer of some value to keep in BIDS (is it full volume? what contrast (T1, T2w)?), I would just call it accordingly with disambiguation in _acq, e.g. anat-T1w_acq-localizer.

2). unfortunately - and . are not yet a part of BIDS. I have filed now an issue about - since I could not find one (although we did have discussions about it in some form). . is trickier one since would mess with file extensions. In ReproIn convention you could definitely have the - but we will replace them with big X to stay compliant with BIDS. May be we should do the same to .?

[satra]

@dlevitas - it may be useful to check how dcm2nii converts the 3 slice localizer. technically i think it will need 3 nifti files. since each orthogonal plane will require a separate qform.

i think it has a single series UID but generates multiple files when converted.

the aascout is different since that doesn't have multiple orientations.

on the naming front in our center - we use reproin with any center specific semantics going after __

[dlevitas]

The localizer does not have any BIDS value; sorry for not specifying that. I've normally used dcmbids/dcm2niix for BIDS conversion in the past, and with that 3 separate nifti files are created for the localizer, which are then discarded and not put into the BIDS folders. Since this specific localizer doesn't have any value, is it just okay then to leave its name as localizer or does it need a heuristic that the program can recognize?

Ah okay, I didn't realize . and - weren't proper BIDS format. For now, I'll stick with underscore, and I noticed in the source code that 0.6mm can be expressed as 060mm I believe. Regardless, we'll leave that peripheral information out of the sequence names for the time being.

[yarikoptic]

1) of you name it anat-scoutacq-localizer I think it will also be ignored as a scout 2) is used by bids to separate entities, don't use it to separate within value!

[dlevitas]

1). okay, we'll go with the anat-scout_acq-localizer for our scouts/localizers 2). Got it, thanks for clarifying.

I think that answers the lingering questions I had. I'll close this out now. Thanks again, @yarikoptic @satra