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ENH: allow _dir for other EPI (func, dwi) sequences
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See bids-standard#47 for initial
brief discussion.

This commit also demonstrates ability to reference other sections within the
document (when referencing fmap Case 4 where _dir described in greater detail
ATM
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@yarikoptic
yarikoptic committed Oct 30, 2018
1 parent ea10d19 commit 2201710
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23 changes: 13 additions & 10 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -185,8 +185,8 @@ Template:
```Text
sub-<participant_label>/[ses-<session_label>/]
func/
sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]
sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_dir-<dir_label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]
sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_dir-<dir_label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
```

Imaging data acquired during BOLD imaging. This includes but is not limited to
Expand Down Expand Up @@ -215,8 +215,11 @@ following names: `sub-01_task-rest_acq-singleband_bold.nii.gz` and
other label than `singleband` and `multiband` as long as they are consistent
across subjects and sessions and consist only of the legal label characters.

Similarly the optional `rec-<label>` key/value can be used to distinguish
different reconstruction algorithms (for example ones using motion correction).
Similarly the optional `dir-<dir_label>` and `rec-<label>` key/values
can be used to distinguish different phase-encoding directions and
reconstruction algorithms (for example ones using motion correction).
See [`fmap` Case 4](01-magnetic-resonance-imaging-data.md#case-4-multiple-phase-encoded-directions-pepolar)
for more information on `dir` field specification.

Multi echo data MUST  be split into one file per echo. Each file shares the same
name with the exception of the `_echo-<index>` key/value. For example:
Expand Down Expand Up @@ -315,12 +318,12 @@ Template:
```Text
sub-<participant_label>/[ses-<session_label>/]
dwi/
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.nii[.gz]
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.bval
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.bvec
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.json
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_sbref.nii[.gz]
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_sbref.json
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_dir-<dir_label>][_run-<index>]_dwi.nii[.gz]
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_dir-<dir_label>][_run-<index>]_dwi.bval
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_dir-<dir_label>][_run-<index>]_dwi.bvec
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_dir-<dir_label>][_run-<index>]_dwi.json
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_dir-<dir_label>][_run-<index>]_sbref.nii[.gz]
sub-<participant_label>[_ses-<session_label>][_acq-<label>][_dir-<dir_label>][_run-<index>]_sbref.json
```

Diffusion-weighted imaging data acquired for that participant. The optional
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2 changes: 1 addition & 1 deletion src/99-appendices/04-entity-table.md
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Expand Up @@ -15,7 +15,7 @@ file type are denoted. Entity formats indicate whether the value is alphanumeric
| Acquisition | `acq-<label>` | Optional | Optional | Optional | Optional | Optional | Optional | Optional | | Optional | Optional |
| Contrast Enhancing Agent | `ce-<label>` | Optional | Optional | | | | | | | | |
| Reconstruction | `rec-<label>` | Optional | Optional | Optional | Optional | | | | | | |
| Phase-Encoding Direction | `dir-<label>` | | | | | | | Required | | | |
| Phase-Encoding Direction | `dir-<label>` | | | Optional | | Optional | | Required | | | |
| Run | `run-<index>` | | | Optional | Optional | Optional | Optional | Optional | | Optional | Optional |
| Corresponding modality | `mod-<label>` | | Optional | | | | | | | | |
| Echo | `echo-<index>` | | | Optional | | | | | | | |
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