From 18a3f2478c86aaa7d10a6834028cb9715c9e091b Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Sat, 16 May 2020 12:42:19 -0400 Subject: [PATCH 01/49] Draft entity and datatype files. --- src/99-appendices/datatypes/anat.yml | 44 +++++++++++++++++++++ src/99-appendices/datatypes/beh.yml | 26 +++++++++++++ src/99-appendices/datatypes/dwi.yml | 32 +++++++++++++++ src/99-appendices/datatypes/eeg.yml | 20 ++++++++++ src/99-appendices/datatypes/fmap.yml | 36 +++++++++++++++++ src/99-appendices/datatypes/func.yml | 58 ++++++++++++++++++++++++++++ src/99-appendices/datatypes/ieeg.yml | 21 ++++++++++ src/99-appendices/datatypes/meg.yml | 24 ++++++++++++ src/99-appendices/entities.yml | 39 +++++++++++++++++++ 9 files changed, 300 insertions(+) create mode 100644 src/99-appendices/datatypes/anat.yml create mode 100644 src/99-appendices/datatypes/beh.yml create mode 100644 src/99-appendices/datatypes/dwi.yml create mode 100644 src/99-appendices/datatypes/eeg.yml create mode 100644 src/99-appendices/datatypes/fmap.yml create mode 100644 src/99-appendices/datatypes/func.yml create mode 100644 src/99-appendices/datatypes/ieeg.yml create mode 100644 src/99-appendices/datatypes/meg.yml create mode 100644 src/99-appendices/entities.yml diff --git a/src/99-appendices/datatypes/anat.yml b/src/99-appendices/datatypes/anat.yml new file mode 100644 index 0000000000..8423179b92 --- /dev/null +++ b/src/99-appendices/datatypes/anat.yml @@ -0,0 +1,44 @@ +group1: + datatypes: + - anat + suffices: + - T1w + - T2w + - T1rho + - T1map + - T2map + - T2star + - FLAIR + - FLASH + - PD + - PDmap + - PDT2 + - inplaneT1 + - inplaneT2 + - angio + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + acq: optional + ce: optional + rec: optional +group2: + datatypes: + - anat + suffices: + - defacemask + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + acq: optional + ce: optional + rec: optional + mod: optional diff --git a/src/99-appendices/datatypes/beh.yml b/src/99-appendices/datatypes/beh.yml new file mode 100644 index 0000000000..5e58a6f2d1 --- /dev/null +++ b/src/99-appendices/datatypes/beh.yml @@ -0,0 +1,26 @@ +group1: + datatypes: + - beh + suffices: + - stim + - physio + extensions: + - tsv.gz + - json + entities: + sub: required + ses: optional + task: required +group2: + datatypes: + - beh + suffices: + - events + - beh + extensions: + - tsv + - json + entities: + sub: required + ses: optional + task: required diff --git a/src/99-appendices/datatypes/dwi.yml b/src/99-appendices/datatypes/dwi.yml new file mode 100644 index 0000000000..13761a6301 --- /dev/null +++ b/src/99-appendices/datatypes/dwi.yml @@ -0,0 +1,32 @@ +group1: + datatypes: + - dwi + suffices: + - dwi + extensions: + - nii.gz + - nii + - json + - bvec + - bval + entities: + sub: required + ses: optional + acq: optional + dir: optional + run: optional +group2: + datatypes: + - dwi + suffices: + - sbref + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + acq: optional + dir: optional + run: optional diff --git a/src/99-appendices/datatypes/eeg.yml b/src/99-appendices/datatypes/eeg.yml new file mode 100644 index 0000000000..8d7a386347 --- /dev/null +++ b/src/99-appendices/datatypes/eeg.yml @@ -0,0 +1,20 @@ +group1: + datatypes: + - eeg + suffices: + - eeg + extensions: + - json + - edf + - vhdr + - vmrk + - eeg + - set + - fdt + - bdf + entities: + sub: required + ses: optional + task: required + acq: optional + run: optional diff --git a/src/99-appendices/datatypes/fmap.yml b/src/99-appendices/datatypes/fmap.yml new file mode 100644 index 0000000000..06ce5b8622 --- /dev/null +++ b/src/99-appendices/datatypes/fmap.yml @@ -0,0 +1,36 @@ +group1: + datatypes: + - fmap + suffices: + - phasediff + - phase1 + - phase2 + - magnitude1 + - magnitude2 + - magnitude + - fieldmap + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + acq: optional + run: optional +group2: + datatypes: + - fmap + suffices: + - epi + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + acq: optional + ce: optional + dir: required + run: optional diff --git a/src/99-appendices/datatypes/func.yml b/src/99-appendices/datatypes/func.yml new file mode 100644 index 0000000000..f10d1d8601 --- /dev/null +++ b/src/99-appendices/datatypes/func.yml @@ -0,0 +1,58 @@ +group1: + datatypes: + - func + suffices: + - bold + - cbv + - phase + - sbref + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + task: required + acq: optional + ce: optional + rec: optional + dir: optional + run: optional + echo: optional +group2: + datatypes: + - func + suffices: + - events + extensions: + - tsv + - json + entities: + sub: required + ses: optional + task: required + acq: optional + ce: optional + rec: optional + dir: optional + run: optional + echo: optional +group3: + datatypes: + - func + suffices: + - physio + - stim + extensions: + - tsv.gz + - json + entities: + sub: required + ses: optional + task: required + acq: optional + rec: optional + run: optional + recording: optional + proc: optional diff --git a/src/99-appendices/datatypes/ieeg.yml b/src/99-appendices/datatypes/ieeg.yml new file mode 100644 index 0000000000..6bc3a81686 --- /dev/null +++ b/src/99-appendices/datatypes/ieeg.yml @@ -0,0 +1,21 @@ +group1: + datatypes: + - ieeg + suffices: + - ieeg + extensions: + - json + - edf + - vhdr + - eeg + - vmrk + - set + - fdt + - nwb + - mef + entities: + sub: required + ses: optional + task: required + acq: optional + run: optional diff --git a/src/99-appendices/datatypes/meg.yml b/src/99-appendices/datatypes/meg.yml new file mode 100644 index 0000000000..73bbb3b4b6 --- /dev/null +++ b/src/99-appendices/datatypes/meg.yml @@ -0,0 +1,24 @@ +group1: + datatypes: + - meg + suffices: + - meg + extensions: + - json + - ctf/ + - fif + - 4d/ + - sqd + - con + - raw + - ave + - mrk + - kdf + - mhd + entities: + sub: required + ses: optional + task: required + acq: optional + run: optional + proc: optional diff --git a/src/99-appendices/entities.yml b/src/99-appendices/entities.yml new file mode 100644 index 0000000000..969cffbdee --- /dev/null +++ b/src/99-appendices/entities.yml @@ -0,0 +1,39 @@ +sub: + description: Subject + format: label +ses: + description: Session + format: label +task: + description: Task + format: label +acq: + description: Acquisition + format: label +ce: + description: Contrast Enhancing Agent + format: label +rec: + description: Reconstruction + format: label +dir: + description: Phase-Encoding Direction + format: label +run: + description: Run + format: index +mod: + description: Corresponding Modality + format: label +echo: + description: Echo + format: index +recording: + description: Recording + format: label +proc: + description: Processed (on device) + format: label +space: + description: Space + format: label From 02c3403c56ebe242cf9cec19778f21cf44cc4e7d Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Sat, 16 May 2020 14:47:32 -0400 Subject: [PATCH 02/49] Draft more specifications. --- src/99-appendices/datatypes/channels.yml | 15 +++++++++++++ src/99-appendices/datatypes/electrodes.yml | 14 ++++++++++++ src/99-appendices/datatypes/events.yml | 15 +++++++++++++ src/99-appendices/datatypes/meg.yml | 26 ++++++++++++++++++++++ src/99-appendices/datatypes/photo.yml | 13 +++++++++++ 5 files changed, 83 insertions(+) create mode 100644 src/99-appendices/datatypes/channels.yml create mode 100644 src/99-appendices/datatypes/electrodes.yml create mode 100644 src/99-appendices/datatypes/events.yml create mode 100644 src/99-appendices/datatypes/photo.yml diff --git a/src/99-appendices/datatypes/channels.yml b/src/99-appendices/datatypes/channels.yml new file mode 100644 index 0000000000..2d9aba87e7 --- /dev/null +++ b/src/99-appendices/datatypes/channels.yml @@ -0,0 +1,15 @@ +group1: + datatypes: + - meg + - eeg + - ieeg + suffices: + - channels + extensions: + - json + - tsv + entities: + sub: required + ses: optional + task: required + run: optional diff --git a/src/99-appendices/datatypes/electrodes.yml b/src/99-appendices/datatypes/electrodes.yml new file mode 100644 index 0000000000..55bcdd52e3 --- /dev/null +++ b/src/99-appendices/datatypes/electrodes.yml @@ -0,0 +1,14 @@ +group1: + datatypes: + - eeg + - ieeg + suffices: + - electrodes + extensions: + - json + - tsv + entities: + sub: required + ses: optional + acq: optional + space: optional diff --git a/src/99-appendices/datatypes/events.yml b/src/99-appendices/datatypes/events.yml new file mode 100644 index 0000000000..98f19d9da9 --- /dev/null +++ b/src/99-appendices/datatypes/events.yml @@ -0,0 +1,15 @@ +group1: + datatypes: + - meg + - eeg + - ieeg + suffices: + - events + extensions: + - json + - tsv + entities: + sub: required + ses: optional + task: required + run: optional diff --git a/src/99-appendices/datatypes/meg.yml b/src/99-appendices/datatypes/meg.yml index 73bbb3b4b6..bcff0dfc64 100644 --- a/src/99-appendices/datatypes/meg.yml +++ b/src/99-appendices/datatypes/meg.yml @@ -22,3 +22,29 @@ group1: acq: optional run: optional proc: optional +group2: + datatypes: + - meg + suffices: + - headshape + extensions: + - pos + - txt + entities: + sub: required + ses: optional + acq: optional + space: optional +group3: + datatypes: + - meg + suffices: + - markers + extensions: + - json + entities: + sub: required + ses: optional + task: optional + acq: optional + space: optional diff --git a/src/99-appendices/datatypes/photo.yml b/src/99-appendices/datatypes/photo.yml new file mode 100644 index 0000000000..2172d7ef91 --- /dev/null +++ b/src/99-appendices/datatypes/photo.yml @@ -0,0 +1,13 @@ +group1: + datatypes: + - meg + - eeg + - ieeg + suffices: + - photo + extensions: + - jpg + entities: + sub: required + ses: optional + acq: optional From 6ea0dfdb1759abb3c9ae2214378cb1403ecb3a6d Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Sat, 16 May 2020 14:58:38 -0400 Subject: [PATCH 03/49] Add specifications for top-level files and directories. --- src/99-appendices/associated_data.yml | 4 ++++ src/99-appendices/top_level_files.yml | 32 +++++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 src/99-appendices/associated_data.yml create mode 100644 src/99-appendices/top_level_files.yml diff --git a/src/99-appendices/associated_data.yml b/src/99-appendices/associated_data.yml new file mode 100644 index 0000000000..5452625aa4 --- /dev/null +++ b/src/99-appendices/associated_data.yml @@ -0,0 +1,4 @@ +- code/ +- derivatives/ +- sourcedata/ +- stimuli/ diff --git a/src/99-appendices/top_level_files.yml b/src/99-appendices/top_level_files.yml new file mode 100644 index 0000000000..e51d2fc359 --- /dev/null +++ b/src/99-appendices/top_level_files.yml @@ -0,0 +1,32 @@ +README: + extensions: + - md + - rst + - None +CHANGES: + extensions: + - md + - rst + - None +dataset_description: + extensions: + - json +genetic_info: + extensions: + - json +participants: + extensions: + - tsv + - json +phasediff: + extensions: + - json +phase1: + extensions: + - json +phase2: + extensions: + - json +fieldmap: + extensions: + - json From 6626368b3030bf854a1b96fd801a38f69c9c243f Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Sun, 17 May 2020 12:37:43 -0400 Subject: [PATCH 04/49] Reorganize yaml files. --- src/{99-appendices => schema}/associated_data.yml | 0 src/{99-appendices => schema}/datatypes/anat.yml | 0 src/{99-appendices => schema}/datatypes/beh.yml | 0 src/{99-appendices => schema}/datatypes/channels.yml | 0 src/{99-appendices => schema}/datatypes/dwi.yml | 0 src/{99-appendices => schema}/datatypes/eeg.yml | 0 src/{99-appendices => schema}/datatypes/electrodes.yml | 0 src/{99-appendices => schema}/datatypes/events.yml | 0 src/{99-appendices => schema}/datatypes/fmap.yml | 0 src/{99-appendices => schema}/datatypes/func.yml | 0 src/{99-appendices => schema}/datatypes/ieeg.yml | 0 src/{99-appendices => schema}/datatypes/meg.yml | 0 src/{99-appendices => schema}/datatypes/photo.yml | 0 src/{99-appendices => schema}/entities.yml | 0 src/{99-appendices => schema}/top_level_files.yml | 0 15 files changed, 0 insertions(+), 0 deletions(-) rename src/{99-appendices => schema}/associated_data.yml (100%) rename src/{99-appendices => schema}/datatypes/anat.yml (100%) rename src/{99-appendices => schema}/datatypes/beh.yml (100%) rename src/{99-appendices => schema}/datatypes/channels.yml (100%) rename src/{99-appendices => schema}/datatypes/dwi.yml (100%) rename src/{99-appendices => schema}/datatypes/eeg.yml (100%) rename src/{99-appendices => schema}/datatypes/electrodes.yml (100%) rename src/{99-appendices => schema}/datatypes/events.yml (100%) rename src/{99-appendices => schema}/datatypes/fmap.yml (100%) rename src/{99-appendices => schema}/datatypes/func.yml (100%) rename src/{99-appendices => schema}/datatypes/ieeg.yml (100%) rename src/{99-appendices => schema}/datatypes/meg.yml (100%) rename src/{99-appendices => schema}/datatypes/photo.yml (100%) rename src/{99-appendices => schema}/entities.yml (100%) rename src/{99-appendices => schema}/top_level_files.yml (100%) diff --git a/src/99-appendices/associated_data.yml b/src/schema/associated_data.yml similarity index 100% rename from src/99-appendices/associated_data.yml rename to src/schema/associated_data.yml diff --git a/src/99-appendices/datatypes/anat.yml b/src/schema/datatypes/anat.yml similarity index 100% rename from src/99-appendices/datatypes/anat.yml rename to src/schema/datatypes/anat.yml diff --git a/src/99-appendices/datatypes/beh.yml b/src/schema/datatypes/beh.yml similarity index 100% rename from src/99-appendices/datatypes/beh.yml rename to src/schema/datatypes/beh.yml diff --git a/src/99-appendices/datatypes/channels.yml b/src/schema/datatypes/channels.yml similarity index 100% rename from src/99-appendices/datatypes/channels.yml rename to src/schema/datatypes/channels.yml diff --git a/src/99-appendices/datatypes/dwi.yml b/src/schema/datatypes/dwi.yml similarity index 100% rename from src/99-appendices/datatypes/dwi.yml rename to src/schema/datatypes/dwi.yml diff --git a/src/99-appendices/datatypes/eeg.yml b/src/schema/datatypes/eeg.yml similarity index 100% rename from src/99-appendices/datatypes/eeg.yml rename to src/schema/datatypes/eeg.yml diff --git a/src/99-appendices/datatypes/electrodes.yml b/src/schema/datatypes/electrodes.yml similarity index 100% rename from src/99-appendices/datatypes/electrodes.yml rename to src/schema/datatypes/electrodes.yml diff --git a/src/99-appendices/datatypes/events.yml b/src/schema/datatypes/events.yml similarity index 100% rename from src/99-appendices/datatypes/events.yml rename to src/schema/datatypes/events.yml diff --git a/src/99-appendices/datatypes/fmap.yml b/src/schema/datatypes/fmap.yml similarity index 100% rename from src/99-appendices/datatypes/fmap.yml rename to src/schema/datatypes/fmap.yml diff --git a/src/99-appendices/datatypes/func.yml b/src/schema/datatypes/func.yml similarity index 100% rename from src/99-appendices/datatypes/func.yml rename to src/schema/datatypes/func.yml diff --git a/src/99-appendices/datatypes/ieeg.yml b/src/schema/datatypes/ieeg.yml similarity index 100% rename from src/99-appendices/datatypes/ieeg.yml rename to src/schema/datatypes/ieeg.yml diff --git a/src/99-appendices/datatypes/meg.yml b/src/schema/datatypes/meg.yml similarity index 100% rename from src/99-appendices/datatypes/meg.yml rename to src/schema/datatypes/meg.yml diff --git a/src/99-appendices/datatypes/photo.yml b/src/schema/datatypes/photo.yml similarity index 100% rename from src/99-appendices/datatypes/photo.yml rename to src/schema/datatypes/photo.yml diff --git a/src/99-appendices/entities.yml b/src/schema/entities.yml similarity index 100% rename from src/99-appendices/entities.yml rename to src/schema/entities.yml diff --git a/src/99-appendices/top_level_files.yml b/src/schema/top_level_files.yml similarity index 100% rename from src/99-appendices/top_level_files.yml rename to src/schema/top_level_files.yml From 5c26565dc66c00e4618e74b73d91e9acc397c003 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 19 May 2020 10:22:21 -0400 Subject: [PATCH 05/49] Add inclusion for top level files. --- src/schema/top_level_files.yml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/schema/top_level_files.yml b/src/schema/top_level_files.yml index e51d2fc359..5d4b177d1a 100644 --- a/src/schema/top_level_files.yml +++ b/src/schema/top_level_files.yml @@ -1,32 +1,41 @@ README: + required: True extensions: - md - rst - None CHANGES: + required: True extensions: - md - rst - None dataset_description: + required: True extensions: - json genetic_info: + required: False extensions: - json participants: + required: True extensions: - tsv - json phasediff: + required: False extensions: - json phase1: + required: False extensions: - json phase2: + required: False extensions: - json fieldmap: + required: False extensions: - json From d6601e71ec278924ce8d4e4b9a27d900b2cf5a6f Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Thu, 21 May 2020 20:04:37 -0400 Subject: [PATCH 06/49] Rename yaml files and add required field. --- src/schema/associated_data.yaml | 8 ++++++++ src/schema/associated_data.yml | 4 ---- src/schema/datatypes/{anat.yml => anat.yaml} | 0 src/schema/datatypes/{beh.yml => beh.yaml} | 0 src/schema/datatypes/{channels.yml => channels.yaml} | 0 src/schema/datatypes/{dwi.yml => dwi.yaml} | 0 src/schema/datatypes/{eeg.yml => eeg.yaml} | 0 src/schema/datatypes/{electrodes.yml => electrodes.yaml} | 0 src/schema/datatypes/{events.yml => events.yaml} | 0 src/schema/datatypes/{fmap.yml => fmap.yaml} | 0 src/schema/datatypes/{func.yml => func.yaml} | 0 src/schema/datatypes/{ieeg.yml => ieeg.yaml} | 0 src/schema/datatypes/{meg.yml => meg.yaml} | 0 src/schema/datatypes/{photo.yml => photo.yaml} | 0 src/schema/{entities.yml => entities.yaml} | 0 src/schema/{top_level_files.yml => top_level_files.yaml} | 2 +- 16 files changed, 9 insertions(+), 5 deletions(-) create mode 100644 src/schema/associated_data.yaml delete mode 100644 src/schema/associated_data.yml rename src/schema/datatypes/{anat.yml => anat.yaml} (100%) rename src/schema/datatypes/{beh.yml => beh.yaml} (100%) rename src/schema/datatypes/{channels.yml => channels.yaml} (100%) rename src/schema/datatypes/{dwi.yml => dwi.yaml} (100%) rename src/schema/datatypes/{eeg.yml => eeg.yaml} (100%) rename src/schema/datatypes/{electrodes.yml => electrodes.yaml} (100%) rename src/schema/datatypes/{events.yml => events.yaml} (100%) rename src/schema/datatypes/{fmap.yml => fmap.yaml} (100%) rename src/schema/datatypes/{func.yml => func.yaml} (100%) rename src/schema/datatypes/{ieeg.yml => ieeg.yaml} (100%) rename src/schema/datatypes/{meg.yml => meg.yaml} (100%) rename src/schema/datatypes/{photo.yml => photo.yaml} (100%) rename src/schema/{entities.yml => entities.yaml} (100%) rename src/schema/{top_level_files.yml => top_level_files.yaml} (96%) diff --git a/src/schema/associated_data.yaml b/src/schema/associated_data.yaml new file mode 100644 index 0000000000..25d3ac8c5d --- /dev/null +++ b/src/schema/associated_data.yaml @@ -0,0 +1,8 @@ +- code/: + - required: False +- derivatives/: + - required: False +- sourcedata/: + - required: False +- stimuli/: + - required: False diff --git a/src/schema/associated_data.yml b/src/schema/associated_data.yml deleted file mode 100644 index 5452625aa4..0000000000 --- a/src/schema/associated_data.yml +++ /dev/null @@ -1,4 +0,0 @@ -- code/ -- derivatives/ -- sourcedata/ -- stimuli/ diff --git a/src/schema/datatypes/anat.yml b/src/schema/datatypes/anat.yaml similarity index 100% rename from src/schema/datatypes/anat.yml rename to src/schema/datatypes/anat.yaml diff --git a/src/schema/datatypes/beh.yml b/src/schema/datatypes/beh.yaml similarity index 100% rename from src/schema/datatypes/beh.yml rename to src/schema/datatypes/beh.yaml diff --git a/src/schema/datatypes/channels.yml b/src/schema/datatypes/channels.yaml similarity index 100% rename from src/schema/datatypes/channels.yml rename to src/schema/datatypes/channels.yaml diff --git a/src/schema/datatypes/dwi.yml b/src/schema/datatypes/dwi.yaml similarity index 100% rename from src/schema/datatypes/dwi.yml rename to src/schema/datatypes/dwi.yaml diff --git a/src/schema/datatypes/eeg.yml b/src/schema/datatypes/eeg.yaml similarity index 100% rename from src/schema/datatypes/eeg.yml rename to src/schema/datatypes/eeg.yaml diff --git a/src/schema/datatypes/electrodes.yml b/src/schema/datatypes/electrodes.yaml similarity index 100% rename from src/schema/datatypes/electrodes.yml rename to src/schema/datatypes/electrodes.yaml diff --git a/src/schema/datatypes/events.yml b/src/schema/datatypes/events.yaml similarity index 100% rename from src/schema/datatypes/events.yml rename to src/schema/datatypes/events.yaml diff --git a/src/schema/datatypes/fmap.yml b/src/schema/datatypes/fmap.yaml similarity index 100% rename from src/schema/datatypes/fmap.yml rename to src/schema/datatypes/fmap.yaml diff --git a/src/schema/datatypes/func.yml b/src/schema/datatypes/func.yaml similarity index 100% rename from src/schema/datatypes/func.yml rename to src/schema/datatypes/func.yaml diff --git a/src/schema/datatypes/ieeg.yml b/src/schema/datatypes/ieeg.yaml similarity index 100% rename from src/schema/datatypes/ieeg.yml rename to src/schema/datatypes/ieeg.yaml diff --git a/src/schema/datatypes/meg.yml b/src/schema/datatypes/meg.yaml similarity index 100% rename from src/schema/datatypes/meg.yml rename to src/schema/datatypes/meg.yaml diff --git a/src/schema/datatypes/photo.yml b/src/schema/datatypes/photo.yaml similarity index 100% rename from src/schema/datatypes/photo.yml rename to src/schema/datatypes/photo.yaml diff --git a/src/schema/entities.yml b/src/schema/entities.yaml similarity index 100% rename from src/schema/entities.yml rename to src/schema/entities.yaml diff --git a/src/schema/top_level_files.yml b/src/schema/top_level_files.yaml similarity index 96% rename from src/schema/top_level_files.yml rename to src/schema/top_level_files.yaml index 5d4b177d1a..7870fd6e1a 100644 --- a/src/schema/top_level_files.yml +++ b/src/schema/top_level_files.yaml @@ -19,7 +19,7 @@ genetic_info: extensions: - json participants: - required: True + required: False extensions: - tsv - json From ee9535faf11f6ecc36ca94f43db57694347f1b3a Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Thu, 21 May 2020 20:05:12 -0400 Subject: [PATCH 07/49] Convert dict to list in example file. --- src/schema/datatypes/anat.yaml | 89 +++++++++++++++++----------------- 1 file changed, 45 insertions(+), 44 deletions(-) diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml index 8423179b92..1867c40816 100644 --- a/src/schema/datatypes/anat.yaml +++ b/src/schema/datatypes/anat.yaml @@ -1,44 +1,45 @@ -group1: - datatypes: - - anat - suffices: - - T1w - - T2w - - T1rho - - T1map - - T2map - - T2star - - FLAIR - - FLASH - - PD - - PDmap - - PDT2 - - inplaneT1 - - inplaneT2 - - angio - extensions: - - nii.gz - - nii - - json - entities: - sub: required - ses: optional - acq: optional - ce: optional - rec: optional -group2: - datatypes: - - anat - suffices: - - defacemask - extensions: - - nii.gz - - nii - - json - entities: - sub: required - ses: optional - acq: optional - ce: optional - rec: optional - mod: optional +groups: +# First group + - datatypes: + - anat + suffices: + - T1w + - T2w + - T1rho + - T1map + - T2map + - T2star + - FLAIR + - FLASH + - PD + - PDmap + - PDT2 + - inplaneT1 + - inplaneT2 + - angio + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + acq: optional + ce: optional + rec: optional +# Second group + - datatypes: + - anat + suffices: + - defacemask + extensions: + - nii.gz + - nii + - json + entities: + sub: required + ses: optional + acq: optional + ce: optional + rec: optional + mod: optional From 56a42b6701484c0fb8e5994006eb4518c00b39dc Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 21 May 2020 21:57:02 -0400 Subject: [PATCH 08/49] [DATALAD RUNCMD] Replace suffices with suffixes === Do not change lines below === { "chain": [], "cmd": "git-sedi suffices suffixes", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "src/schema" } ^^^ Do not change lines above ^^^ --- src/schema/datatypes/anat.yaml | 4 ++-- src/schema/datatypes/beh.yaml | 4 ++-- src/schema/datatypes/channels.yaml | 2 +- src/schema/datatypes/dwi.yaml | 4 ++-- src/schema/datatypes/eeg.yaml | 2 +- src/schema/datatypes/electrodes.yaml | 2 +- src/schema/datatypes/events.yaml | 2 +- src/schema/datatypes/fmap.yaml | 4 ++-- src/schema/datatypes/func.yaml | 6 +++--- src/schema/datatypes/ieeg.yaml | 2 +- src/schema/datatypes/meg.yaml | 6 +++--- src/schema/datatypes/photo.yaml | 2 +- 12 files changed, 20 insertions(+), 20 deletions(-) diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml index 1867c40816..506bcf8192 100644 --- a/src/schema/datatypes/anat.yaml +++ b/src/schema/datatypes/anat.yaml @@ -2,7 +2,7 @@ groups: # First group - datatypes: - anat - suffices: + suffixes: - T1w - T2w - T1rho @@ -30,7 +30,7 @@ groups: # Second group - datatypes: - anat - suffices: + suffixes: - defacemask extensions: - nii.gz diff --git a/src/schema/datatypes/beh.yaml b/src/schema/datatypes/beh.yaml index 5e58a6f2d1..2015e19735 100644 --- a/src/schema/datatypes/beh.yaml +++ b/src/schema/datatypes/beh.yaml @@ -1,7 +1,7 @@ group1: datatypes: - beh - suffices: + suffixes: - stim - physio extensions: @@ -14,7 +14,7 @@ group1: group2: datatypes: - beh - suffices: + suffixes: - events - beh extensions: diff --git a/src/schema/datatypes/channels.yaml b/src/schema/datatypes/channels.yaml index 2d9aba87e7..fedd4e5ce0 100644 --- a/src/schema/datatypes/channels.yaml +++ b/src/schema/datatypes/channels.yaml @@ -3,7 +3,7 @@ group1: - meg - eeg - ieeg - suffices: + suffixes: - channels extensions: - json diff --git a/src/schema/datatypes/dwi.yaml b/src/schema/datatypes/dwi.yaml index 13761a6301..0c62cdea33 100644 --- a/src/schema/datatypes/dwi.yaml +++ b/src/schema/datatypes/dwi.yaml @@ -1,7 +1,7 @@ group1: datatypes: - dwi - suffices: + suffixes: - dwi extensions: - nii.gz @@ -18,7 +18,7 @@ group1: group2: datatypes: - dwi - suffices: + suffixes: - sbref extensions: - nii.gz diff --git a/src/schema/datatypes/eeg.yaml b/src/schema/datatypes/eeg.yaml index 8d7a386347..7b8aac2b1e 100644 --- a/src/schema/datatypes/eeg.yaml +++ b/src/schema/datatypes/eeg.yaml @@ -1,7 +1,7 @@ group1: datatypes: - eeg - suffices: + suffixes: - eeg extensions: - json diff --git a/src/schema/datatypes/electrodes.yaml b/src/schema/datatypes/electrodes.yaml index 55bcdd52e3..87a6983252 100644 --- a/src/schema/datatypes/electrodes.yaml +++ b/src/schema/datatypes/electrodes.yaml @@ -2,7 +2,7 @@ group1: datatypes: - eeg - ieeg - suffices: + suffixes: - electrodes extensions: - json diff --git a/src/schema/datatypes/events.yaml b/src/schema/datatypes/events.yaml index 98f19d9da9..25d8c9c5e5 100644 --- a/src/schema/datatypes/events.yaml +++ b/src/schema/datatypes/events.yaml @@ -3,7 +3,7 @@ group1: - meg - eeg - ieeg - suffices: + suffixes: - events extensions: - json diff --git a/src/schema/datatypes/fmap.yaml b/src/schema/datatypes/fmap.yaml index 06ce5b8622..0767791150 100644 --- a/src/schema/datatypes/fmap.yaml +++ b/src/schema/datatypes/fmap.yaml @@ -1,7 +1,7 @@ group1: datatypes: - fmap - suffices: + suffixes: - phasediff - phase1 - phase2 @@ -21,7 +21,7 @@ group1: group2: datatypes: - fmap - suffices: + suffixes: - epi extensions: - nii.gz diff --git a/src/schema/datatypes/func.yaml b/src/schema/datatypes/func.yaml index f10d1d8601..2519e33c09 100644 --- a/src/schema/datatypes/func.yaml +++ b/src/schema/datatypes/func.yaml @@ -1,7 +1,7 @@ group1: datatypes: - func - suffices: + suffixes: - bold - cbv - phase @@ -23,7 +23,7 @@ group1: group2: datatypes: - func - suffices: + suffixes: - events extensions: - tsv @@ -41,7 +41,7 @@ group2: group3: datatypes: - func - suffices: + suffixes: - physio - stim extensions: diff --git a/src/schema/datatypes/ieeg.yaml b/src/schema/datatypes/ieeg.yaml index 6bc3a81686..ae4878c127 100644 --- a/src/schema/datatypes/ieeg.yaml +++ b/src/schema/datatypes/ieeg.yaml @@ -1,7 +1,7 @@ group1: datatypes: - ieeg - suffices: + suffixes: - ieeg extensions: - json diff --git a/src/schema/datatypes/meg.yaml b/src/schema/datatypes/meg.yaml index bcff0dfc64..d4221b0280 100644 --- a/src/schema/datatypes/meg.yaml +++ b/src/schema/datatypes/meg.yaml @@ -1,7 +1,7 @@ group1: datatypes: - meg - suffices: + suffixes: - meg extensions: - json @@ -25,7 +25,7 @@ group1: group2: datatypes: - meg - suffices: + suffixes: - headshape extensions: - pos @@ -38,7 +38,7 @@ group2: group3: datatypes: - meg - suffices: + suffixes: - markers extensions: - json diff --git a/src/schema/datatypes/photo.yaml b/src/schema/datatypes/photo.yaml index 2172d7ef91..40ae993927 100644 --- a/src/schema/datatypes/photo.yaml +++ b/src/schema/datatypes/photo.yaml @@ -3,7 +3,7 @@ group1: - meg - eeg - ieeg - suffices: + suffixes: - photo extensions: - jpg From 596ed002de85a24f2f6bae68fae2853ed5f7daf0 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 3 Jun 2020 10:58:41 -0400 Subject: [PATCH 09/49] Add leading "." to extensions to match specification. --- src/schema/datatypes/anat.yaml | 12 ++++++------ src/schema/datatypes/beh.yaml | 8 ++++---- src/schema/datatypes/channels.yaml | 4 ++-- src/schema/datatypes/dwi.yaml | 16 ++++++++-------- src/schema/datatypes/eeg.yaml | 16 ++++++++-------- src/schema/datatypes/electrodes.yaml | 4 ++-- src/schema/datatypes/events.yaml | 4 ++-- src/schema/datatypes/fmap.yaml | 12 ++++++------ src/schema/datatypes/func.yaml | 14 +++++++------- src/schema/datatypes/ieeg.yaml | 18 +++++++++--------- src/schema/datatypes/meg.yaml | 26 +++++++++++++------------- src/schema/datatypes/photo.yaml | 2 +- src/schema/top_level_files.yaml | 22 +++++++++++----------- 13 files changed, 79 insertions(+), 79 deletions(-) diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml index 506bcf8192..bb1e4eec9d 100644 --- a/src/schema/datatypes/anat.yaml +++ b/src/schema/datatypes/anat.yaml @@ -18,9 +18,9 @@ groups: - inplaneT2 - angio extensions: - - nii.gz - - nii - - json + - .nii.gz + - .nii + - .json entities: sub: required ses: optional @@ -33,9 +33,9 @@ groups: suffixes: - defacemask extensions: - - nii.gz - - nii - - json + - .nii.gz + - .nii + - .json entities: sub: required ses: optional diff --git a/src/schema/datatypes/beh.yaml b/src/schema/datatypes/beh.yaml index 2015e19735..71474c3e05 100644 --- a/src/schema/datatypes/beh.yaml +++ b/src/schema/datatypes/beh.yaml @@ -5,8 +5,8 @@ group1: - stim - physio extensions: - - tsv.gz - - json + - .tsv.gz + - .json entities: sub: required ses: optional @@ -18,8 +18,8 @@ group2: - events - beh extensions: - - tsv - - json + - .tsv + - .json entities: sub: required ses: optional diff --git a/src/schema/datatypes/channels.yaml b/src/schema/datatypes/channels.yaml index fedd4e5ce0..83143121fb 100644 --- a/src/schema/datatypes/channels.yaml +++ b/src/schema/datatypes/channels.yaml @@ -6,8 +6,8 @@ group1: suffixes: - channels extensions: - - json - - tsv + - .json + - .tsv entities: sub: required ses: optional diff --git a/src/schema/datatypes/dwi.yaml b/src/schema/datatypes/dwi.yaml index 0c62cdea33..f42ad46db8 100644 --- a/src/schema/datatypes/dwi.yaml +++ b/src/schema/datatypes/dwi.yaml @@ -4,11 +4,11 @@ group1: suffixes: - dwi extensions: - - nii.gz - - nii - - json - - bvec - - bval + - .nii.gz + - .nii + - .json + - .bvec + - .bval entities: sub: required ses: optional @@ -21,9 +21,9 @@ group2: suffixes: - sbref extensions: - - nii.gz - - nii - - json + - .nii.gz + - .nii + - .json entities: sub: required ses: optional diff --git a/src/schema/datatypes/eeg.yaml b/src/schema/datatypes/eeg.yaml index 7b8aac2b1e..6bc9d2d1dc 100644 --- a/src/schema/datatypes/eeg.yaml +++ b/src/schema/datatypes/eeg.yaml @@ -4,14 +4,14 @@ group1: suffixes: - eeg extensions: - - json - - edf - - vhdr - - vmrk - - eeg - - set - - fdt - - bdf + - .json + - .edf + - .vhdr + - .vmrk + - .eeg + - .set + - .fdt + - .bdf entities: sub: required ses: optional diff --git a/src/schema/datatypes/electrodes.yaml b/src/schema/datatypes/electrodes.yaml index 87a6983252..96cc4d36dc 100644 --- a/src/schema/datatypes/electrodes.yaml +++ b/src/schema/datatypes/electrodes.yaml @@ -5,8 +5,8 @@ group1: suffixes: - electrodes extensions: - - json - - tsv + - .json + - .tsv entities: sub: required ses: optional diff --git a/src/schema/datatypes/events.yaml b/src/schema/datatypes/events.yaml index 25d8c9c5e5..53e1555c0c 100644 --- a/src/schema/datatypes/events.yaml +++ b/src/schema/datatypes/events.yaml @@ -6,8 +6,8 @@ group1: suffixes: - events extensions: - - json - - tsv + - .json + - .tsv entities: sub: required ses: optional diff --git a/src/schema/datatypes/fmap.yaml b/src/schema/datatypes/fmap.yaml index 0767791150..3400fe0446 100644 --- a/src/schema/datatypes/fmap.yaml +++ b/src/schema/datatypes/fmap.yaml @@ -10,9 +10,9 @@ group1: - magnitude - fieldmap extensions: - - nii.gz - - nii - - json + - .nii.gz + - .nii + - .json entities: sub: required ses: optional @@ -24,9 +24,9 @@ group2: suffixes: - epi extensions: - - nii.gz - - nii - - json + - .nii.gz + - .nii + - .json entities: sub: required ses: optional diff --git a/src/schema/datatypes/func.yaml b/src/schema/datatypes/func.yaml index 2519e33c09..e5f0ca5e9a 100644 --- a/src/schema/datatypes/func.yaml +++ b/src/schema/datatypes/func.yaml @@ -7,9 +7,9 @@ group1: - phase - sbref extensions: - - nii.gz - - nii - - json + - .nii.gz + - .nii + - .json entities: sub: required ses: optional @@ -26,8 +26,8 @@ group2: suffixes: - events extensions: - - tsv - - json + - .tsv + - .json entities: sub: required ses: optional @@ -45,8 +45,8 @@ group3: - physio - stim extensions: - - tsv.gz - - json + - .tsv.gz + - .json entities: sub: required ses: optional diff --git a/src/schema/datatypes/ieeg.yaml b/src/schema/datatypes/ieeg.yaml index ae4878c127..af424d1745 100644 --- a/src/schema/datatypes/ieeg.yaml +++ b/src/schema/datatypes/ieeg.yaml @@ -4,15 +4,15 @@ group1: suffixes: - ieeg extensions: - - json - - edf - - vhdr - - eeg - - vmrk - - set - - fdt - - nwb - - mef + - .json + - .edf + - .vhdr + - .eeg + - .vmrk + - .set + - .fdt + - .nwb + - .mef entities: sub: required ses: optional diff --git a/src/schema/datatypes/meg.yaml b/src/schema/datatypes/meg.yaml index d4221b0280..5b7b7aa481 100644 --- a/src/schema/datatypes/meg.yaml +++ b/src/schema/datatypes/meg.yaml @@ -4,17 +4,17 @@ group1: suffixes: - meg extensions: - - json - - ctf/ - - fif - 4d/ - - sqd - - con - - raw - - ave - - mrk - - kdf - - mhd + - ctf/ + - .json + - .fif + - .sqd + - .con + - .raw + - .ave + - .mrk + - .kdf + - .mhd entities: sub: required ses: optional @@ -28,8 +28,8 @@ group2: suffixes: - headshape extensions: - - pos - - txt + - .pos + - .txt entities: sub: required ses: optional @@ -41,7 +41,7 @@ group3: suffixes: - markers extensions: - - json + - .json entities: sub: required ses: optional diff --git a/src/schema/datatypes/photo.yaml b/src/schema/datatypes/photo.yaml index 40ae993927..799e2fb8db 100644 --- a/src/schema/datatypes/photo.yaml +++ b/src/schema/datatypes/photo.yaml @@ -6,7 +6,7 @@ group1: suffixes: - photo extensions: - - jpg + - .jpg entities: sub: required ses: optional diff --git a/src/schema/top_level_files.yaml b/src/schema/top_level_files.yaml index 7870fd6e1a..66e5e48510 100644 --- a/src/schema/top_level_files.yaml +++ b/src/schema/top_level_files.yaml @@ -1,41 +1,41 @@ README: required: True extensions: - - md - - rst + - .md + - .rst - None CHANGES: required: True extensions: - - md - - rst + - .md + - .rst - None dataset_description: required: True extensions: - - json + - .json genetic_info: required: False extensions: - - json + - .json participants: required: False extensions: - tsv - - json + - .json phasediff: required: False extensions: - - json + - .json phase1: required: False extensions: - - json + - .json phase2: required: False extensions: - - json + - .json fieldmap: required: False extensions: - - json + - .json From 45fdfca4a10489d91802e63a843ae75d328435db Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 3 Jun 2020 11:13:24 -0400 Subject: [PATCH 10/49] Convert dict to list. --- src/schema/datatypes/anat.yaml | 85 +++++++++++++++++----------------- 1 file changed, 42 insertions(+), 43 deletions(-) diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml index bb1e4eec9d..ba57891737 100644 --- a/src/schema/datatypes/anat.yaml +++ b/src/schema/datatypes/anat.yaml @@ -1,45 +1,44 @@ -groups: # First group - - datatypes: - - anat - suffixes: - - T1w - - T2w - - T1rho - - T1map - - T2map - - T2star - - FLAIR - - FLASH - - PD - - PDmap - - PDT2 - - inplaneT1 - - inplaneT2 - - angio - extensions: - - .nii.gz - - .nii - - .json - entities: - sub: required - ses: optional - acq: optional - ce: optional - rec: optional +- datatypes: + - anat + suffixes: + - T1w + - T2w + - T1rho + - T1map + - T2map + - T2star + - FLAIR + - FLASH + - PD + - PDmap + - PDT2 + - inplaneT1 + - inplaneT2 + - angio + extensions: + - .nii.gz + - .nii + - .json + entities: + sub: required + ses: optional + acq: optional + ce: optional + rec: optional # Second group - - datatypes: - - anat - suffixes: - - defacemask - extensions: - - .nii.gz - - .nii - - .json - entities: - sub: required - ses: optional - acq: optional - ce: optional - rec: optional - mod: optional +- datatypes: + - anat + suffixes: + - defacemask + extensions: + - .nii.gz + - .nii + - .json + entities: + sub: required + ses: optional + acq: optional + ce: optional + rec: optional + mod: optional From 9ec4e09e5818a0c80fd156fc96de742b80bbe467 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 3 Jun 2020 11:16:29 -0400 Subject: [PATCH 11/49] Fix iEEG extension based on issue. --- src/schema/datatypes/ieeg.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/datatypes/ieeg.yaml b/src/schema/datatypes/ieeg.yaml index af424d1745..3b9971e11b 100644 --- a/src/schema/datatypes/ieeg.yaml +++ b/src/schema/datatypes/ieeg.yaml @@ -4,6 +4,7 @@ group1: suffixes: - ieeg extensions: + - .mefd/ - .json - .edf - .vhdr @@ -12,7 +13,6 @@ group1: - .set - .fdt - .nwb - - .mef entities: sub: required ses: optional From d03d895500d1e91d1e81e931ccb6e0696ff80df6 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 3 Jun 2020 15:15:32 -0400 Subject: [PATCH 12/49] Split auxdatatypes and drop datatypes key. --- .../{datatypes => auxdatatypes}/channels.yaml | 3 +-- .../{datatypes => auxdatatypes}/electrodes.yaml | 3 +-- .../{datatypes => auxdatatypes}/events.yaml | 3 +-- src/schema/{datatypes => auxdatatypes}/photo.yaml | 3 +-- src/schema/datatypes/anat.yaml | 8 ++------ src/schema/datatypes/beh.yaml | 10 ++-------- src/schema/datatypes/dwi.yaml | 10 ++-------- src/schema/datatypes/eeg.yaml | 5 +---- src/schema/datatypes/fmap.yaml | 10 ++-------- src/schema/datatypes/func.yaml | 15 +++------------ src/schema/datatypes/ieeg.yaml | 5 +---- src/schema/datatypes/meg.yaml | 15 +++------------ 12 files changed, 20 insertions(+), 70 deletions(-) rename src/schema/{datatypes => auxdatatypes}/channels.yaml (89%) rename src/schema/{datatypes => auxdatatypes}/electrodes.yaml (89%) rename src/schema/{datatypes => auxdatatypes}/events.yaml (89%) rename src/schema/{datatypes => auxdatatypes}/photo.yaml (87%) diff --git a/src/schema/datatypes/channels.yaml b/src/schema/auxdatatypes/channels.yaml similarity index 89% rename from src/schema/datatypes/channels.yaml rename to src/schema/auxdatatypes/channels.yaml index 83143121fb..990221c253 100644 --- a/src/schema/datatypes/channels.yaml +++ b/src/schema/auxdatatypes/channels.yaml @@ -1,5 +1,4 @@ -group1: - datatypes: +- datatypes: - meg - eeg - ieeg diff --git a/src/schema/datatypes/electrodes.yaml b/src/schema/auxdatatypes/electrodes.yaml similarity index 89% rename from src/schema/datatypes/electrodes.yaml rename to src/schema/auxdatatypes/electrodes.yaml index 96cc4d36dc..afe6b7495b 100644 --- a/src/schema/datatypes/electrodes.yaml +++ b/src/schema/auxdatatypes/electrodes.yaml @@ -1,5 +1,4 @@ -group1: - datatypes: +- datatypes: - eeg - ieeg suffixes: diff --git a/src/schema/datatypes/events.yaml b/src/schema/auxdatatypes/events.yaml similarity index 89% rename from src/schema/datatypes/events.yaml rename to src/schema/auxdatatypes/events.yaml index 53e1555c0c..0d0e02434c 100644 --- a/src/schema/datatypes/events.yaml +++ b/src/schema/auxdatatypes/events.yaml @@ -1,5 +1,4 @@ -group1: - datatypes: +- datatypes: - meg - eeg - ieeg diff --git a/src/schema/datatypes/photo.yaml b/src/schema/auxdatatypes/photo.yaml similarity index 87% rename from src/schema/datatypes/photo.yaml rename to src/schema/auxdatatypes/photo.yaml index 799e2fb8db..df333510d4 100644 --- a/src/schema/datatypes/photo.yaml +++ b/src/schema/auxdatatypes/photo.yaml @@ -1,5 +1,4 @@ -group1: - datatypes: +- datatypes: - meg - eeg - ieeg diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml index ba57891737..d072221f93 100644 --- a/src/schema/datatypes/anat.yaml +++ b/src/schema/datatypes/anat.yaml @@ -1,7 +1,5 @@ # First group -- datatypes: - - anat - suffixes: +- suffixes: - T1w - T2w - T1rho @@ -27,9 +25,7 @@ ce: optional rec: optional # Second group -- datatypes: - - anat - suffixes: +- suffixes: - defacemask extensions: - .nii.gz diff --git a/src/schema/datatypes/beh.yaml b/src/schema/datatypes/beh.yaml index 71474c3e05..55c55b51f0 100644 --- a/src/schema/datatypes/beh.yaml +++ b/src/schema/datatypes/beh.yaml @@ -1,7 +1,4 @@ -group1: - datatypes: - - beh - suffixes: +- suffixes: - stim - physio extensions: @@ -11,10 +8,7 @@ group1: sub: required ses: optional task: required -group2: - datatypes: - - beh - suffixes: +- suffixes: - events - beh extensions: diff --git a/src/schema/datatypes/dwi.yaml b/src/schema/datatypes/dwi.yaml index f42ad46db8..e50311bb6f 100644 --- a/src/schema/datatypes/dwi.yaml +++ b/src/schema/datatypes/dwi.yaml @@ -1,7 +1,4 @@ -group1: - datatypes: - - dwi - suffixes: +- suffixes: - dwi extensions: - .nii.gz @@ -15,10 +12,7 @@ group1: acq: optional dir: optional run: optional -group2: - datatypes: - - dwi - suffixes: +- suffixes: - sbref extensions: - .nii.gz diff --git a/src/schema/datatypes/eeg.yaml b/src/schema/datatypes/eeg.yaml index 6bc9d2d1dc..20f163ac2c 100644 --- a/src/schema/datatypes/eeg.yaml +++ b/src/schema/datatypes/eeg.yaml @@ -1,7 +1,4 @@ -group1: - datatypes: - - eeg - suffixes: +- suffixes: - eeg extensions: - .json diff --git a/src/schema/datatypes/fmap.yaml b/src/schema/datatypes/fmap.yaml index 3400fe0446..009a708b80 100644 --- a/src/schema/datatypes/fmap.yaml +++ b/src/schema/datatypes/fmap.yaml @@ -1,7 +1,4 @@ -group1: - datatypes: - - fmap - suffixes: +- suffixes: - phasediff - phase1 - phase2 @@ -18,10 +15,7 @@ group1: ses: optional acq: optional run: optional -group2: - datatypes: - - fmap - suffixes: +- suffixes: - epi extensions: - .nii.gz diff --git a/src/schema/datatypes/func.yaml b/src/schema/datatypes/func.yaml index e5f0ca5e9a..9052487cee 100644 --- a/src/schema/datatypes/func.yaml +++ b/src/schema/datatypes/func.yaml @@ -1,7 +1,4 @@ -group1: - datatypes: - - func - suffixes: +- suffixes: - bold - cbv - phase @@ -20,10 +17,7 @@ group1: dir: optional run: optional echo: optional -group2: - datatypes: - - func - suffixes: +- suffixes: - events extensions: - .tsv @@ -38,10 +32,7 @@ group2: dir: optional run: optional echo: optional -group3: - datatypes: - - func - suffixes: +- suffixes: - physio - stim extensions: diff --git a/src/schema/datatypes/ieeg.yaml b/src/schema/datatypes/ieeg.yaml index 3b9971e11b..f9351d6a5d 100644 --- a/src/schema/datatypes/ieeg.yaml +++ b/src/schema/datatypes/ieeg.yaml @@ -1,7 +1,4 @@ -group1: - datatypes: - - ieeg - suffixes: +- suffixes: - ieeg extensions: - .mefd/ diff --git a/src/schema/datatypes/meg.yaml b/src/schema/datatypes/meg.yaml index 5b7b7aa481..d37e99b98c 100644 --- a/src/schema/datatypes/meg.yaml +++ b/src/schema/datatypes/meg.yaml @@ -1,7 +1,4 @@ -group1: - datatypes: - - meg - suffixes: +- suffixes: - meg extensions: - 4d/ @@ -22,10 +19,7 @@ group1: acq: optional run: optional proc: optional -group2: - datatypes: - - meg - suffixes: +- suffixes: - headshape extensions: - .pos @@ -35,10 +29,7 @@ group2: ses: optional acq: optional space: optional -group3: - datatypes: - - meg - suffixes: +- suffixes: - markers extensions: - .json From 8d3436c08043334507cae8add167b4382165e444 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 3 Jun 2020 17:11:00 -0400 Subject: [PATCH 13/49] Add descriptions to entities. --- src/schema/entities.yaml | 100 +++++++++++++++++++++++++++----- src/schema/top_level_files.yaml | 2 +- 2 files changed, 88 insertions(+), 14 deletions(-) diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml index 969cffbdee..cb6cf67566 100644 --- a/src/schema/entities.yaml +++ b/src/schema/entities.yaml @@ -1,39 +1,113 @@ sub: - description: Subject + name: Subject + description: "A person or animal participating in the study." format: label ses: - description: Session + name: Session + description: "A logical grouping of neuroimaging and behavioral data + consistent across subjects. + Session can (but doesn't have to) be synonymous to a visit in a + longitudinal study. + In general, subjects will stay in the scanner during one session. + However, for example, if a subject has to leave the scanner room + and then be re-positioned on the scanner bed, the set of MRI + acquisitions will still be considered as a session and match + sessions acquired in other subjects. + Similarly, in situations where different data types are obtained + over several visits (for example fMRI on one day followed by DWI + the day after) those can be grouped in one session. + Defining multiple sessions is appropriate when several identical + or similar data acquisitions are planned and performed on all + -or most- subjects, often in the case of some intervention between + sessions (e.g., training)." format: label task: - description: Task + name: Task format: label + description: "Each task has a unique label that MUST only consist of letters + and/or numbers (other characters, including spaces and + underscores, are not allowed). + Those labels MUST be consistent across subjects and sessions." acq: - description: Acquisition + name: Acquisition + description: "The OPTIONAL acq-