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Briana Oshiro {briana.oshiro@uconn.edu} committed Feb 21, 2020
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1 change: 1 addition & 0 deletions bids/.bidsignore
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extra_data/
5 changes: 5 additions & 0 deletions bids/README
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A free form text ( README ) describing the dataset in more details that SHOULD be provided

The raw BIDS data was created using BIDScoin 2.3
All provenance information and settings can be found in ./code/bidscoin
For more information see: https://github.com/Donders-Institute/bidscoin
14 changes: 14 additions & 0 deletions bids/code/bidscoin/bidscoiner.errors
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2020-02-21 13:02:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" (errorcode 0)
2020-02-21 13:02:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag" (errorcode 0)
2020-02-21 13:02:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor" (errorcode 0)
2020-02-21 13:02:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra" (errorcode 0)
2020-02-21 13:02:38 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-1_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" (errorcode 0)
2020-02-21 13:02:38 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-music_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" (errorcode 0)
2020-02-21 13:03:12 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-music_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" (errorcode 0)
2020-02-21 13:03:12 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-music_acq-SequenceName_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers_physio" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/008-task-music_PhysioLog" (errorcode 2)
2020-02-21 13:03:12 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-prosody_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" (errorcode 0)
2020-02-21 13:03:13 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-prosody_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" (errorcode 0)
2020-02-21 13:03:13 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-prosody_acq-SequenceName_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers_physio" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/011-task-prosody_PhysioLog" (errorcode 2)
2020-02-21 13:03:13 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-prosody_acq-epfid2d184_dir-COL_run-2_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" (errorcode 0)
2020-02-21 13:03:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-prosody_acq-epfid2d184_dir-COL_run-2_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" (errorcode 0)
2020-02-21 13:03:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-prosody_acq-SequenceName_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers_physio" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/014-task-prosody_PhysioLog" (errorcode 2)
197 changes: 197 additions & 0 deletions bids/code/bidscoin/bidscoiner.log
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366 changes: 366 additions & 0 deletions bids/code/bidscoin/bidsmap.yaml
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# --------------------------------------------------------------------------------
# This is a bidsmap YAML file with the key-value mappings for the different BIDS
# modalities (anat, func, dwi, etc). The modality attributes are the keys that map
# onto the BIDS labels. The bidsmap data-structure should be 5 levels deep:
# dict > dict > list > dict > dict
#
# NB:
# 1) Edit the bidsmap file to your needs before feeding it to bidscoiner.py
# 2) (Institute) users may create their own bidsmap_[template].yaml or
# bidsmap_[sample].yaml file
#
# For more information, see:
# https://github.com/Donders-Institute/bidscoin
# https://docs.ansible.com/ansible/latest/reference_appendices/YAMLSyntax.html
# --------------------------------------------------------------------------------


Options:
# --------------------------------------------------------------------------------
# General options
# --------------------------------------------------------------------------------
bidscoin:
version: '2.3' # BIDScoin version (should correspond with the version in ../bidscoin/version.txt)
bidsignore: extra_data/ # Semicolon-separated list of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. extra_data/;pet/;myfile.txt;yourfile.csv
dcm2niix: # See dcm2niix -h and https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage for more info
path: /usr/local/bin/ # Command to set the path to dcm2niix (note the semi-colon), e.g. module add dcm2niix/1.0.20180622; or PATH=/opt/dcm2niix/bin:$PATH; or /opt/dcm2niix/bin/ or '"C:\Program Files\dcm2niix\"' (note the quotes to deal with the whitespace)
args: -b y -z y -i n # Argument string that is passed to dcm2niix. Tip: SPM users may want to use '-z n' (which produces unzipped nifti's, see dcm2niix -h for more information)


PlugIns: []
# --------------------------------------------------------------------------------
# List of plugins to edit the key-value heuristics / perform additional operations
# --------------------------------------------------------------------------------
#- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder

PlugIn:
# --------------------------------------------------------------------------------
# List of plugins to edit the key-value heuristics / perform additional operations
# --------------------------------------------------------------------------------
#- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder


DICOM:
# --------------------------------------------------------------------------------
# DICOM key-value heuristics (DICOM fields that are mapped to the BIDS labels)
# --------------------------------------------------------------------------------
subject: <<SourceFilePath>> # <<SourceFilePath>> extracts the subject label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as subject-label instead, e.g. <PatientID>
session: <<SourceFilePath>> # <<SourceFilePath>> extracts the session label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as session-label instead, e.g. <StudyID>
anat: # ----------------------- All anatomical series --------------------
- provenance: /data/raw/sub-TD902TD/005-T1w/TD^TD902TD_005_T1w_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: T1w
SeriesDescription: T1w
ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']"
SequenceName: '*tfl3d1_16ns'
SequenceVariant: "['SK', 'SP', 'MP']"
ScanningSequence: "['GR', 'IR']"
MRAcquisitionType: 3D
SliceThickness: '1'
FlipAngle: '9'
EchoNumbers: 1
EchoTime: '2.98'
RepetitionTime: '2300'
PhaseEncodingDirection: ''
bids:
acq: ''
ce:
rec:
run: <<1>>
mod:
suffix: T1w
func: # ----------------------- All functional series --------------------
- provenance: /data/raw/sub-TD902TD/006-task-music_SBRef/TD^TD902TD_006_task-music_SBRef_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: task-music
SeriesDescription: task-music_SBRef
ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']"
SequenceName: epfid2d1_84
SequenceVariant: "['SK', 'SS']"
ScanningSequence: EP
MRAcquisitionType: 2D
SliceThickness: '2.5'
FlipAngle: '45'
EchoNumbers: 1
EchoTime: '30.2'
RepetitionTime: '1070'
PhaseEncodingDirection: ''
bids:
suffix: sbref
task: music
acq: epfid2d184
ce:
dir: COL
rec:
run: <<1>>
echo: '1'
- provenance: /data/raw/sub-TD902TD/007-task-music/TD^TD902TD_007_task-music_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: task-music
SeriesDescription: task-music
ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']"
SequenceName: epfid2d1_84
SequenceVariant: "['SK', 'SS']"
ScanningSequence: EP
MRAcquisitionType: 2D
SliceThickness: '2.5'
FlipAngle: '45'
EchoNumbers: 1
EchoTime: '30.2'
RepetitionTime: '1070'
PhaseEncodingDirection: ''
bids:
task: music
acq: epfid2d184
ce:
dir: COL
rec:
run: <<1>>
echo: '1'
suffix: bold
- provenance: /data/raw/sub-TD902TD/008-task-music_PhysioLog/TD^TD902TD_008_task-music_PhysioLog_00927_00001.dcm
attributes:
Modality: MR
ProtocolName: task-music
SeriesDescription: task-music_PhysioLog
ImageType: "['ORIGINAL', 'PRIMARY', 'RAWDATA', 'PHYSIO']"
SequenceName: ''
SequenceVariant: ''
ScanningSequence: ''
MRAcquisitionType: ''
SliceThickness: ''
FlipAngle: ''
EchoNumbers: ''
EchoTime: ''
RepetitionTime: ''
PhaseEncodingDirection: ''
bids:
suffix: physio
task: music
acq: <SequenceName>
ce:
dir: <InPlanePhaseEncodingDirection>
rec:
run: <<1>>
echo: <EchoNumbers>
- provenance: /data/raw/sub-TD902TD/009-task-prosody_SBRef/TD^TD902TD_009_task-prosody_SBRef_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: task-prosody
SeriesDescription: task-prosody_SBRef
ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']"
SequenceName: epfid2d1_84
SequenceVariant: "['SK', 'SS']"
ScanningSequence: EP
MRAcquisitionType: 2D
SliceThickness: '2.5'
FlipAngle: '45'
EchoNumbers: 1
EchoTime: '30.2'
RepetitionTime: '1070'
PhaseEncodingDirection: ''
bids:
suffix: sbref
task: prosody
acq: epfid2d184
ce:
dir: COL
rec:
run: <<1>>
echo: '1'
- provenance: /data/raw/sub-TD902TD/010-task-prosody/TD^TD902TD_010_task-prosody_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: task-prosody
SeriesDescription: task-prosody
ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']"
SequenceName: epfid2d1_84
SequenceVariant: "['SK', 'SS']"
ScanningSequence: EP
MRAcquisitionType: 2D
SliceThickness: '2.5'
FlipAngle: '45'
EchoNumbers: 1
EchoTime: '30.2'
RepetitionTime: '1070'
PhaseEncodingDirection: ''
bids:
task: prosody
acq: epfid2d184
ce:
dir: COL
rec:
run: <<1>>
echo: '1'
suffix: bold
- provenance: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog/TD^TD902TD_011_task-prosody_PhysioLog_00046_00001.dcm
attributes:
Modality: MR
ProtocolName: task-prosody
SeriesDescription: task-prosody_PhysioLog
ImageType: "['ORIGINAL', 'PRIMARY', 'RAWDATA', 'PHYSIO']"
SequenceName: ''
SequenceVariant: ''
ScanningSequence: ''
MRAcquisitionType: ''
SliceThickness: ''
FlipAngle: ''
EchoNumbers: ''
EchoTime: ''
RepetitionTime: ''
PhaseEncodingDirection: ''
bids:
suffix: physio
task: prosody
acq: <SequenceName>
ce:
dir: <InPlanePhaseEncodingDirection>
rec:
run: <<1>>
echo: <EchoNumbers>
dwi: # ----------------------- All diffusion series ---------------------
fmap: # ----------------------- All fieldmap series ----------------------
beh: # ----------------------- All behavioural data ---------------------
pet: # ----------------------- All PET series ---------------------------
extra_data: # ----------------------- All extra data ---------------------------
- provenance: /data/raw/sub-TD902TD/001-AAHead_Scout/TD^TD902TD_001_AAHead_Scout_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: AAHead_Scout
SeriesDescription: AAHead_Scout
ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']"
SequenceName: '*fl3d1_ns'
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '1.6000000238419'
FlipAngle: '8'
EchoNumbers: 1
EchoTime: '1.37'
RepetitionTime: '3.15'
PhaseEncodingDirection: ''
bids:
acq: AAHeadScout
rec:
ce:
task:
echo: '1'
dir: ROW
run: <<1>>
mod:
suffix:
- provenance: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag/TD^TD902TD_002_AAHead_Scout_MPR_sag_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: AAHead_Scout
SeriesDescription: AAHead_Scout_MPR_sag
ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']"
SequenceName: '*fl3d1_ns'
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '1.6000000238419'
FlipAngle: '8'
EchoNumbers: 1
EchoTime: '1.37'
RepetitionTime: '3.15'
PhaseEncodingDirection: ''
bids:
acq: AAHeadScoutMPRsag
rec:
ce:
task:
echo: '1'
dir: <InPlanePhaseEncodingDirection>
run: <<1>>
mod:
suffix:
- provenance: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor/TD^TD902TD_003_AAHead_Scout_MPR_cor_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: AAHead_Scout
SeriesDescription: AAHead_Scout_MPR_cor
ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']"
SequenceName: '*fl3d1_ns'
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '1.6000000238419'
FlipAngle: '8'
EchoNumbers: 1
EchoTime: '1.37'
RepetitionTime: '3.15'
PhaseEncodingDirection: ''
bids:
acq: AAHeadScoutMPRcor
rec:
ce:
task:
echo: '1'
dir: <InPlanePhaseEncodingDirection>
run: <<1>>
mod:
suffix:
- provenance: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra/TD^TD902TD_004_AAHead_Scout_MPR_tra_00001_00001.dcm
attributes:
Modality: MR
ProtocolName: AAHead_Scout
SeriesDescription: AAHead_Scout_MPR_tra
ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']"
SequenceName: '*fl3d1_ns'
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '1.6000000238419'
FlipAngle: '8'
EchoNumbers: 1
EchoTime: '1.37'
RepetitionTime: '3.15'
PhaseEncodingDirection: ''
bids:
acq: AAHeadScoutMPRtra
rec:
ce:
task:
echo: '1'
dir: <InPlanePhaseEncodingDirection>
run: <<1>>
mod:
suffix:
leave_out: # ----------------------- Data that will be left out ---------------
PAR:
# --------------------------------------------------------------------------------
# PAR key-value heuristics (Philips PAR fields that are mapped to the BIDS labels)
# --------------------------------------------------------------------------------


P7:
# --------------------------------------------------------------------------------
# P*.7 key-value heuristics (GE fields that are mapped to the BIDS labels)
# --------------------------------------------------------------------------------


Nifti:
# --------------------------------------------------------------------------------
# Nifti key-value heuristics (Nifti fields that are mapped to the BIDS labels)
# --------------------------------------------------------------------------------


FileSystem:
# --------------------------------------------------------------------------------
# File system key-value heuristics (these file- and foldernames will be mapped
# to the BIDS labels; Special substitutions can be performed using python's
# Format Specification Mini-Language)
# --------------------------------------------------------------------------------
subject: <<SourceFilePath>> # <<SourceFilePath>> extracts the subject label from the source directory during bidscoiner runtime
session: <<SourceFilePath>> # <<SourceFilePath>> extracts the session label from the source directory during bidscoiner runtime
anat: # ----------------------- All anatomical series --------------------
func: # ----------------------- All functional series --------------------
dwi: # ----------------------- All diffusion series ---------------------
fmap: # ----------------------- All fieldmap series ----------------------
beh: # ----------------------- All behavioural data ---------------------
extra_data: # ----------------------- All extra data ---------------------------
leave_out: # ----------------------- Data that will be left out ---------------

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