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ReproIn Convention

ReproIn project is a part of the ReproNim Center suite of tools and frameworks, and was established when DBIC obtained a new Siemens 3T Scanner. ReproIn consists of two parts: a specification on how to organize and name exam cards in the scanner, and a tool to convert acquired DICOMs to BIDS layout.

Specification

The header of the ReproIn heuristic file shipped within HeuDiConv describes details of the specification on how to organize and name study sequences at MR console. Currently it is

Sequence naming on the scanner console

Sequence names on the scanner must follow this specification to avoid manual conversion/handling (split in multiple lines only for visualization, there should be no spaces or new lines in the name):

[PREFIX:][WIP ]<seqtype[-label]>[_ses-<SESID>]
   [_task-<TASKID>][_acq-<ACQLABEL>][_run-<RUNID>][_dir-<DIR>][<more BIDS>]
   [__<custom>]

where

  • [PREFIX:] - leading capital letters followed by ":" are stripped/ignored
  • [WIP ] - prefix is stripped/ignored (added by Philips for patch sequences)
  • <...> - value to be entered
  • [...] - optional -- might be nearly mandatory for some modalities (e.g., _run-<RUNID> for functional) and very optional for others. See BIDS IV. Entity Table
  • *ID - alpha-numerical identifier (e.g., 01, 02, pre, post, pre01) for a run, task, session. Note that makes more sense to use numerical values for RUNID (e.g., _run-01, _run-02) for obvious sorting and possibly descriptive ones for e.g., SESID (_ses-movie, _ses-localizer)

  • <seqtype[-label]> is a known BIDS sequence type which is usually a name of the folder under subject's directory. And (optional) label is specific per sequence type (e.g. typical bold for func, or T1w for anat, fid for mrs), which could often (but not always) be deduced from DICOM. Known to BIDS modalities are:

  • anat - anatomical data. Might also be collected multiple times across runs (e.g. if subject is taken out of magnet etc), so could (optionally) have _run definition attached. For "standard anat" labels, please consult to BIDS specification "Anatomy imaging data" but most common are T1w, T2w, angio,

  • func - functional (AKA task, including resting state) data. Typically contains multiple runs, and might have multiple different tasks different per each run (e.g., _task-memory_run-01, _task-oddball_run-02),
  • fmap - field maps. Could be spin-echo sequences with _dir- (e.g., fmap_dir-AP, fmap_dir-PA),
  • dwi - diffusion weighted imaging (also can as well have runs),
  • mrs - magnetic resonanse spectroscopy (WiP BEP022)

  • _ses-<SESID> (optional) a session. Having a single sequence within a study would make that study follow "multi-session" layout. A common practice to have a _ses specifier within the scout sequence name. You can either specify explicit session identifier (SESID) or just say to maintain, create (starts with 1). You can also use _ses-{date} in case of scanning phantoms or non-human subjects and wanting sessions to be coded by the acquisition date. (see e.g., ///dbic/QA dataset acquired with such session identified).

  • _task-<TASKID> (optional) a short name for a task performed during that run. If not provided and it is a func sequence, _task-UNKNOWN will be automatically added to comply with BIDS. Consult http://www.cognitiveatlas.org/tasks on known tasks.

  • _acq-<ACQLABEL> (optional) a short custom label to distinguish a different set of parameters used for acquiring the same modality (e.g., _acq-highres, _acq-lowres, etc)

  • _run-<RUNID> (optional) a (typically functional) run. The same idea as with SESID.

  • _dir-[AP,PA,LR,RL,VD,DV] (optional) to be used for fmap images, whenever a pair of the SE images is collected to be used to estimate the fieldmap.

  • <more BIDS> (optional) any other fields (e.g., _acq-) from the BIDS specification pertinent to that seqtype.

  • __<custom> (optional) after two underscores any arbitrary comment which will not matter to how layout in BIDS. But that one theoretically should not be necessary, and (ab)use of it would just signal lack of thought while preparing sequence name to start with since everything could have been expressed in BIDS fields.

Last moment checks/FAQ:

  • Functional runs should have _task-<TASKID> field defined
  • It is advisable to avoid using sequential _run-<index> through out different functional tasks -- use separate sequences of run indices within each task. E.g. _task-1_run-01, _task-1_run-02, _task-2_run-01, _task-2_run-02 instead of
    _task-1_run-01, _task-1_run-02, _task-2_run-03, _task-2_run-04.
  • Do not use +, _ or - within SESID, TASKID, ACQLABEL, RUNID, so we could detect "canceled" runs.
  • If run was canceled -- just copy canceled run (with the same index) and re-run it. Files with overlapping name will be considered duplicate/canceled session and only the last one would remain. The others would acquire __dup0<number> suffix.

Although we still support - and + used within SESID and TASKID, their use is not recommended, thus not listed here

The HeuDiConv tool

HeuDiConv is a flexible DICOM converter for organizing brain imaging data into structured directory layouts. ReproIn [heuristic] was developed and now is shipped within HeuDiConv, so it could be used independently of the ReproIn setup on any HeuDiConv installation (specify -f reproin to heudiconv call).

TODO: describe DBIC specific settings etc. if to be done independently. Probably with use of docker and/or singularity

Meta studies

In some cases it might be desired to collect sequences (e.g., localizer runs) from different studies. heudiconv with reproin heuristic could be used there as well, just point to a new dataset (e.g. localizers) and specify empty --locator to avoid re-establishing the original hierarchy. You could provide dicom tarballs from BIDS datasets as input, so something like

heudiconv -f reproin --locator '' --bids --files \ /inbox/BIDS/PI/INV/[0-9]/sourcedata/sub-/func/sub-_task-{ffa,mimetic,ppa,...}.tgz \ -o /inbox/BIDS/PI/INV/localizers

TODO: convert to containerized example TODO: check that it actually works ;)

Samples

MRS

WiP to define sensible names for MRS sequences. BIDS MRS BEP022 is not yet finalized, so we are only self-compliant here

  • svs_GABA_160_rival -> mrs_acq-gaba_task-rival -- produces 3 measurements
  • acq-gaba_task-rival
  • acq-gaba_task-rival_edit-on PulseSequenceTiming + PulseSequencePulses + PulseSequenceName into .json
  • acq-gaba_task-rival_proc-diff svs_se_water_rival -> mrs_spec-unsup svs_se_dummy -> mrs_acq-quick16_spec-sup