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Step 2 — Sequence Naming

The sequences must follow the ReproIn Naming Convention and the BIDS requirements. BIDS filenames are based on BIDS entities (keys), which are paired with a label or index (value). An entity-label pair is connected by a hyphen -, e.g. task-rest. The entity pairs are separated by underscores _, e.g. func-bold_task-rest. Correctly naming your sequences depends on knowing what entities to add to your file name and how to label them, which we explain here.

We first discuss some general guidelines about choosing appropriate labels. Next, to help you correctly name the sequences we provide a selection of naming patterns. Mind that not all possible entities are listed per sequence. To view all, have a look at the BIDS entity table. All sequences and entities listed below are supported by our automated data acquisition pipeline.

General requirements for labels

Every label must be an alphanumeric string in lower case. The only exception is the phase encoding direction where upper case abbreviations are used.

Every index must be numeric.

We recommend the use of the acq label to distinguish or describe the sequence further. This label can be used to highlight important parameters (e.g. voxel size) or to maintain inherited sequence tags (e.g. hcpli for the T1w).

If a sequence with the same name is used multiple times within a session, a run index based on the chronological order is automatically added by the acquisition pipeline. You can add a run index for yourself, but it will be ignored during conversion.

If scouts or localizers are used, their names must start with anat-scout to be handled properly by the conversion pipeline, which means they will not appear in the BIDS repository.

The task label has implications for how BIDS apps and curation tools can further process your data. Therefore, pay attention that:

  • For resting state fMRI sequences task-rest must be used.
  • Any task data that is not labeled task-rest requires valid BIDS event files. See our guide on how to create these.
  • The task label for other tasks should be a short and descriptive name, for example its common name, like task-stroop or task-nback.

Warning

Ensure that task data you want to analyse together has the same task label. This makes further processing easier. For example, if you perform different versions of an n-back task but want to model neural responses for all versions together, label the task nback. If you are still not certain which task label to use, also consider the event files. If you follow our guide on structuring event files, tasks with the same label should always have the same columns.

Naming patterns

The following tables provide the naming patterns. Also see here for examples.

The requirement level column indicates whether an entity must always be added (required), is advisable (recommended), or is optional. Note that optional means we recommend it if applicable. In general, an entity is required when it is necessary to distinguish otherwise identical sequences.

<datatype>-<suffix>_task-<label>_acq-<label>

Component Input Requirement level
<datatype> anat required
<suffix> T1w required
task-<label> label of experiment task optional
acq-<label> acquisition, additional information recommended

e.g.: anat-T1w_task-rest_acq-hcpli

<datatype>-<suffix>_task-<label>_acq-<label>

Component Input Requirement level
<datatype> anat required
<suffix> T2w required
task-<label> label of experiment task optional
acq-<label> acquisition, additional information recommended

e.g.: anat-T2w_task-rest_acq-hcpli

<datatype>-<suffix>_task-<label>_acq-<label>

Component Input Requirement level
<datatype> anat required
<suffix> MP2RAGE required
task-<label> label of experiment task optional
acq-<label> acquisition, additional information recommended

e.g.: anat-MP2RAGE_acq-ssri

The sequence acquires one phasediff and at least one magnitude image. The corresponding suffixes (phasediff, magnitude1 & magnitude2) will be added automatically during DICOM conversion.

<datatype>_acq-<label>

Component Input Requirement level
<datatype> fmap required
acq-<label> acquisition, additional information recommended

e.g.: fmap_acq-gefmsl56

<datatype>-<suffix>_task-<label>_acq-<label>

Component Input Requirement level
<datatype> func required
<suffix> bold required
task-<label> label of experiment task required
acq-<label> acquisition, additional information recommended

e.g.: func-bold_task-rest_acq-mb4mesl56

<datatype>_acq-<label>_dir-<label>

Component Input Requirement level
<datatype> fmap required
<suffix> epi required
acq-<label> acquisition, additional information recommended
dir-<label> phase-encoding direction: e.g. AP, PA, LR... required

e.g.: fmap-epi_acq-6_dir-AP

<datatype>-<suffix>_acq-<label>_dir-<label>

Component Input Requirement level
<datatype> dwi required
<suffix> dwi required
acq-<label> acquisition, additional information recommended
dir-<label> phase-encoding direction: e.g. AP, PA, LR... recommended

Note: Within our conversion pipeline, the phase encoding direction is retrieved from the DICOM header.

e.g.: dwi-dwi_acq-256_dir-AP

Save sequences on site

Once all sequences are planned they can be prepared on site. Store project sequences in a designated project directory labelled with the name of your data repository. If you have sessions that differ in their sequences, you can have multiple directories, one for each session.

Before you continue

  • All sequences are named following the ReproIn/BIDS conventions
  • All labels are lowercase alphanumeric (except phase encoding directions: AP, PA, LR, RL)
  • Every functional sequence has a task-<label>
  • Resting state sequences use task-rest
  • Event files are planned for all non-resting-state functional sequences
  • Scouts start with anat-scout
  • Phase encoding direction is specified for all pepolar fieldmaps and DWI sequences
  • If any sequences are non-standard, the BIDScoin map path is noted for the conversion config