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[FIX] Clarify use of session entity in filenames #532

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merged 5 commits into from
Aug 10, 2020
Merged

[FIX] Clarify use of session entity in filenames #532

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9eda6a4
Clarify when ses-<label> is optional
Moo-Marc Jul 21, 2020
7708479
Clarify when ses-<label> is optional
Moo-Marc Jul 21, 2020
f30d137
Update 01-contributors.md
Moo-Marc Jul 21, 2020
00bf8d5
Revert changes to entity table.
Moo-Marc Aug 5, 2020
60293aa
Update src/02-common-principles.md
Moo-Marc Aug 6, 2020
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4 changes: 3 additions & 1 deletion src/02-common-principles.md
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Expand Up @@ -99,7 +99,9 @@ A file name consists of a chain of *entities*, or key-value pairs, a *suffix* an
Two prominent examples of entities are `subject` and `session`.

For a data file that was collected in a given `session` from a given
`subject`, the file name will begin with the string `sub-<label>_ses-<label>`.
`subject`, the file name MUST begin with the string `sub-<label>_ses-<label>`.
If the `session` level is omitted in the folder structure, the file name MUST begin
with the string `sub-<label>`.
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Note that `sub-<label>` corresponds to the `subject` entity because it has
the `sub-` "key" and`<label>` "value", where `<label>` would in a real data file
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1 change: 1 addition & 0 deletions src/99-appendices/01-contributors.md
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Expand Up @@ -92,6 +92,7 @@ your name is not listed, please add it.
- Gregory Kiar 📖💻🎨🔧
- Robert Knight 📖
- Jean-Philippe Lachaux 📖
- Marc Lalancette 📖
- Pamela LaMontagne 📖💡
- Kevin Larcher 💬
- Jonathan C. Lau 📖
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36 changes: 19 additions & 17 deletions src/99-appendices/04-entity-table.md
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Expand Up @@ -13,20 +13,22 @@ A general introduction to entities is given in the section on
| Entity | Subject | Session | Task | Acquisition | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run | Corresponding modality | Echo | Recording | Processed (on device) | Space | Split |
| :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :-------------------- | :---------------| :-------------- |
| Format | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>` | `rec-<label>` | `dir-<label>` | `run-<index>` | `mod-<label>` | `echo-<index>` | `recording-<label>` | `proc-<label>` | `space-<label>` | `split-<index>` |
| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED | OPTIONAL | | OPTIONAL | OPTIONAL | OPTIONAL | | | | | | | | |
| anat<br>(defacemask) | REQUIRED | OPTIONAL | | OPTIONAL | OPTIONAL | OPTIONAL | | | OPTIONAL | | | | | |
| func<br>(bold cbv phase sbref events) | REQUIRED | OPTIONAL | REQUIRED | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | OPTIONAL | | | | |
| func<br>(physio stim) | REQUIRED | OPTIONAL | REQUIRED | OPTIONAL | | OPTIONAL | | OPTIONAL | | | OPTIONAL | OPTIONAL | | |
| dwi<br>(dwi bvec bval) | REQUIRED | OPTIONAL | | OPTIONAL | | | OPTIONAL | OPTIONAL | | | | | | |
| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap) | REQUIRED | OPTIONAL | | OPTIONAL | | | | OPTIONAL | | | | | | |
| fmap<br>(epi) | REQUIRED | OPTIONAL | | OPTIONAL | OPTIONAL | | REQUIRED | OPTIONAL | | | | | | |
| beh<br>(events stim physio) | REQUIRED | OPTIONAL | REQUIRED | | | | | | | | | | | |
| meg<br> | REQUIRED | OPTIONAL | REQUIRED | OPTIONAL | | | | OPTIONAL | | | | OPTIONAL | | OPTIONAL |
| eeg<br> | REQUIRED | OPTIONAL | REQUIRED | OPTIONAL | | | | OPTIONAL | | | | | | |
| ieeg<br> | REQUIRED | OPTIONAL | REQUIRED | OPTIONAL | | | | OPTIONAL | | | | | | |
| channels<br>(meg/eeg/ieeg) | REQUIRED | OPTIONAL | REQUIRED | | | | | OPTIONAL | | | | | | |
| headshape<br>(meg) | REQUIRED | OPTIONAL | | OPTIONAL | | | | | | | | | OPTIONAL | |
| markers<br>(meg) | REQUIRED | OPTIONAL | OPTIONAL | OPTIONAL | | | | | | | | | OPTIONAL | |
| photo<br>(meg/eeg/ieeg) | REQUIRED | OPTIONAL | | OPTIONAL | | | | | | | | | | |
| electrodes<br>(eeg/ieeg) | REQUIRED | OPTIONAL | | OPTIONAL | | | | | | | | | OPTIONAL | |
| events<br>(meg/eeg/ieeg) | REQUIRED | OPTIONAL | REQUIRED | | | | | OPTIONAL | | | | | | |
| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED | REQUIRED* | | OPTIONAL | OPTIONAL | OPTIONAL | | | | | | | | |
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| anat<br>(defacemask) | REQUIRED | REQUIRED* | | OPTIONAL | OPTIONAL | OPTIONAL | | | OPTIONAL | | | | | |
| func<br>(bold cbv phase sbref events) | REQUIRED | REQUIRED* | REQUIRED | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | OPTIONAL | | OPTIONAL | | | | |
| func<br>(physio stim) | REQUIRED | REQUIRED* | REQUIRED | OPTIONAL | | OPTIONAL | | OPTIONAL | | | OPTIONAL | OPTIONAL | | |
| dwi<br>(dwi bvec bval) | REQUIRED | REQUIRED* | | OPTIONAL | | | OPTIONAL | OPTIONAL | | | | | | |
| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap) | REQUIRED | REQUIRED* | | OPTIONAL | | | | OPTIONAL | | | | | | |
| fmap<br>(epi) | REQUIRED | REQUIRED* | | OPTIONAL | OPTIONAL | | REQUIRED | OPTIONAL | | | | | | |
| beh<br>(events stim physio) | REQUIRED | REQUIRED* | REQUIRED | | | | | | | | | | | |
| meg<br> | REQUIRED | REQUIRED* | REQUIRED | OPTIONAL | | | | OPTIONAL | | | | OPTIONAL | | OPTIONAL |
| eeg<br> | REQUIRED | REQUIRED* | REQUIRED | OPTIONAL | | | | OPTIONAL | | | | | | |
| ieeg<br> | REQUIRED | REQUIRED* | REQUIRED | OPTIONAL | | | | OPTIONAL | | | | | | |
| channels<br>(meg/eeg/ieeg) | REQUIRED | REQUIRED* | REQUIRED | | | | | OPTIONAL | | | | | | |
| headshape<br>(meg) | REQUIRED | REQUIRED* | | OPTIONAL | | | | | | | | | OPTIONAL | |
| markers<br>(meg) | REQUIRED | REQUIRED* | OPTIONAL | OPTIONAL | | | | | | | | | OPTIONAL | |
| photo<br>(meg/eeg/ieeg) | REQUIRED | REQUIRED* | | OPTIONAL | | | | | | | | | | |
| electrodes<br>(eeg/ieeg) | REQUIRED | REQUIRED* | | OPTIONAL | | | | | | | | | OPTIONAL | |
| events<br>(meg/eeg/ieeg) | REQUIRED | REQUIRED* | REQUIRED | | | | | OPTIONAL | | | | | | |

\*The session entity is REQUIRED when the session level is present in the folder structure. It MUST NOT be used otherwise.