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hw2 yi
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Yi Wei {yi.wei@uconn.edu}
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Feb 21, 2020
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extra_data/ |
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A free form text ( README ) describing the dataset in more details that SHOULD be provided | ||
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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 |
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2020-02-21 13:10:51 - 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 13:10:52 - 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 13:10:52 - 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 13:10:52 - 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 13:10:58 - 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 13:10:58 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_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 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_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 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskmusicPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/008-task-music_PhysioLog" (errorcode 2) | ||
2020-02-21 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_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 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_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 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/011-task-prosody_PhysioLog" (errorcode 2) | ||
2020-02-21 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_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 13:12:09 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_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 13:12:09 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/014-task-prosody_PhysioLog" (errorcode 2) |
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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 | ||
# -------------------------------------------------------------------------------- | ||
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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) | ||
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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 | ||
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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 | ||
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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: taskmusic | ||
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: taskmusic | ||
acq: epfid2d184 | ||
ce: | ||
dir: COL | ||
rec: | ||
run: <<1>> | ||
echo: '1' | ||
suffix: bold | ||
- 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: taskprosody | ||
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: taskprosody | ||
acq: epfid2d184 | ||
ce: | ||
dir: COL | ||
rec: | ||
run: <<1>> | ||
echo: '1' | ||
suffix: bold | ||
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: | ||
- 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: | ||
acq: taskmusicPhysioLog | ||
rec: | ||
ce: | ||
task: | ||
echo: <EchoNumbers> | ||
dir: <InPlanePhaseEncodingDirection> | ||
run: <<1>> | ||
mod: | ||
suffix: | ||
- 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: | ||
acq: taskprosodyPhysioLog | ||
rec: | ||
ce: | ||
task: | ||
echo: <EchoNumbers> | ||
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) | ||
# -------------------------------------------------------------------------------- | ||
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P7: | ||
# -------------------------------------------------------------------------------- | ||
# P*.7 key-value heuristics (GE fields that are mapped to the BIDS labels) | ||
# -------------------------------------------------------------------------------- | ||
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Nifti: | ||
# -------------------------------------------------------------------------------- | ||
# Nifti key-value heuristics (Nifti fields that are mapped to the BIDS labels) | ||
# -------------------------------------------------------------------------------- | ||
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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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