Step 2: Sequence naming
The sequences must follow the ReproIn Naming Convention and the BIDS requirements. BIDS filenames are based on BIDS entities, which are further explained on the next page. In the file name each BIDS entity is paired with a label or index, which is split from the entity name by a hyphen -
. The entities themselves are separated by underscores _
. 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 a 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).
You do not need to copy a sequence when you plan on using it multiple times in the same session. When one sequence is used multiple times in the same session, a run index is automatically added by the acquisition pipeline.
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 analyze together has the same task label. This makes further processing easier. For example, if you perform different versions of an n-back task but you want to model the neural responses for all these 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 provides information if an entity needs to be added to the sequence name in any case (required), we recommend to add it (recommended) or if it is optional. Note that optional means we recommended 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>_flip-<index>_inv-<index>
Component | Input | Requirement level |
---|---|---|
<datatype> |
anat | required |
<suffix> |
MP2RAGE | required |
task-<label> |
label of experiment task | optional |
acq-<label> |
acquisition, additional information | recommended |
flip-<index> |
flip angle: integer | optional |
inv-<index> |
inversion time: nonnegative integer | required |
e.g.: anat-MP2RAGE_acq-ssri_flip-10_inv-1
<datatype>_acq-<label>
Component | Input | Requirement level |
---|---|---|
<datatype> |
fmap | required |
acq-<label> |
acquisition, additional information | recommended |
As the phasediff and two magnitudes usually result from one sequence, BIDS adds the corresponding suffixes later.
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 | optional |
acq-<label> |
acquisition, additional information | recommended |
e.g.: func-bold_task-rest_acq-mb4mesl56
<datatype>-<suffix>_task-<label>_acq-<label>_dir-<label>
Component | Input | Requirement level |
---|---|---|
<datatype> |
dwi | required |
<suffix> |
dwi | required |
task-<label> |
label of experiment task | optional |
acq-<label> |
acquisition, additional information | recommended |
dir-<label> |
phase-encoding direction: e.g. AP, PA, LR... | optional |
Note: Within our conversion pipeline, the Phase Encoding Direction gets retrieved from the DICOM header.
e.g.: dwi-dwi_acq-256_dir-AP