Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[FIX] Drop _part- reference from example, introduce _split- entity #460

Merged
merged 7 commits into from
May 19, 2020
Merged

[FIX] Drop _part- reference from example, introduce _split- entity #460

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
9bd1f0e
FIX: clarify _part
sappelhoff May 4, 2020
38f47e1
update entity table
sappelhoff May 4, 2020
638a2fe
inject _part into MEG spec
sappelhoff May 4, 2020
37c1ced
Update src/99-appendices/06-meg-file-formats.md
teonbrooks May 8, 2020
731aced
drop _part-, introduce _split-
sappelhoff May 12, 2020
0bd8a6a
label -> index
sappelhoff May 13, 2020
fd7b8d4
Apply suggestions from code review
sappelhoff May 16, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 12 additions & 5 deletions src/04-modality-specific-files/02-magnetoencephalography.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,11 +42,18 @@ MAY be included alongside the MEG data; examples are provided below.
This template is for MEG data of any kind, including but not limited to
task-based, resting-state, and noise recordings. If multiple Tasks were
performed within a single Run, the task description can be set to
`task-multitask`. The \_meg.json SHOULD contain details on the Tasks. Some
manufacturers data storage conventions use folders which contain data files of
various nature: e.g., CTF’s .ds format, or BTi/4D. Please refer to
[Appendix VI](../99-appendices/06-meg-file-formats.md) for examples from a
selection of MEG manufacturers.
`task-multitask`. The \_meg.json SHOULD contain details on the Tasks.

Some manufacturers' data storage conventions use folders which contain data
files of various nature: for example, CTF's `.ds` format, or BTi/4D.
Yet other manufacturers split their files once they exceed a certain size
limit. For example Neuromag/Elekta/Megin, which can produce several files
for a single recording. Both `some_file.fif` and `some_file-1.fif` would
belong to a single recording. In BIDS, the `split` entity is RECOMMENDED to
deal with split files.
Please refer to [Appendix VI](../99-appendices/06-meg-file-formats.md) for
general information on how to deal with such manufacturer specifics and to see
more examples.

The `proc` label is analogous to `rec` for MR and denotes a variant of a file
that was a result of particular processing performed on the device. This is
Expand Down
40 changes: 20 additions & 20 deletions src/99-appendices/04-entity-table.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,23 +10,23 @@ file type are denoted. Entity formats indicate whether the value is alphanumeric
A general introduction to entities is given in the section on
[file name structure](../02-common-principles.md#file-name-structure)

| Entity | Subject | Session | Task | Acquisition | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run | Corresponding modality | Echo | Recording | Processed (on device) | Space |
| :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :-------------------- | :---------------|
| 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>` |
| 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 | |
| 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 | | | | | |
| 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 | | | | | | |
37 changes: 20 additions & 17 deletions src/99-appendices/06-meg-file-formats.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -88,32 +88,35 @@ sub-control01_ses-001_task-rest_run-01_proc-sss_meg.fif
sub-control01_ses-001_task-rest_run-01_proc-sss_meg.json
```

In the case of data runs exceeding 2Gb, the data is stored in two separate
files:
In the case of long data recordings that exceed a file size of 2Gb, the `.fif`
files are conventionally split into multiple parts. For example:

```Text
sub-control01_ses-001_task-rest_run-01_meg.fif
sub-control01_ses-001_task-rest_run-01_meg-1.fif
some_file.fif
some_file-1.fif
```

Each of these two files has a pointer to the next file. In some software
applications, like [MNE](https://www.martinos.org/mne/stable/index.html), one
can simply specify the name of the first file, and data will be read in both
files via this pointer. For this reason, it is RECOMMENDED to rename and write
back the file once read, to avoid the persistence of a pointer associated with
the old file name.
Each of these files has an internal pointer to the next file.
This is important when renaming these split recordings to the BIDS convention.
Instead of a simple renaming, files should be read in and saved under their new
names with dedicated tools like [MNE](https://mne.tools), which will ensure
that not only the file names, but also the internal file pointers will be
updated.

Naming convention:
It is RECOMMENDED that `.fif` files with multiple parts use the `split-<index>`
entity to indicate each part.
teonbrooks marked this conversation as resolved.
Show resolved Hide resolved

Example:

```Text
sub-control01_ses-001_task-rest_run-01_part-01_meg.fif
sub-control01_ses-001_task-rest_run-01_part-02_meg.fif
sub-control01_ses-001_task-rest_run-01_split-01_meg.fif
sub-control01_ses-001_task-rest_run-01_split-02_meg.fif
```

More about the Neuromag/Elekta/MEGIN data organization at:
[http://www.fieldtriptoolbox.org/getting_started/neuromag](http://www.fieldtriptoolbox.org/getting_started/neuromag)
And BabyMEG :
[http://www.fieldtriptoolbox.org/getting_started/babysquid](http://www.fieldtriptoolbox.org/getting_started/babysquid)
More information can be found under the following links:

- [Neuromag/Elekta/MEGIN data organization](http://www.fieldtriptoolbox.org/getting_started/neuromag)
- [BabyMEG](http://www.fieldtriptoolbox.org/getting_started/babysquid)

## BTi/4D neuroimaging

Expand Down