-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbidsmap.yaml
181 lines (171 loc) · 7.17 KB
/
bidsmap.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
# --------------------------------------------------------------------------------
# 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: 2.3.1 # 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: dcm2niix; # 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: []
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: ~
attributes:
Modality: MR
ProtocolName: ~
SeriesDescription: '*t1*'
ImageType: '*M*'
SequenceName: ~
SequenceVariant: ~
ScanningSequence: ~
MRAcquisitionType: ~
SliceThickness: ~
FlipAngle: ~
EchoNumbers: ~
EchoTime: ~
RepetitionTime: ~
PhaseEncodingDirection: ~
bids:
acq: t1
rec:
ce:
task:
echo: <EchoNumber>
dir:
run: <AcquisitionNumber>
mod:
suffix: magnitude
- provenance: ~
attributes:
Modality: MR
ProtocolName: ~
SeriesDescription: '*T1*'
ImageType: ~
SequenceName: ~
SequenceVariant: ~
ScanningSequence: ~
MRAcquisitionType: ~
SliceThickness: ~
FlipAngle: ~
EchoNumbers: ~
EchoTime: ~
RepetitionTime: ~
PhaseEncodingDirection: ~
bids:
acq: t1
rec:
ce:
task:
echo: <EchoNumber>
dir:
run: <AcquisitionNumber>
mod:
suffix: magnitude
- provenance: ~
attributes:
Modality: MR
ProtocolName: ~
SeriesDescription: ~
ImageType: '*M*'
SequenceName: ~
SequenceVariant: ~
ScanningSequence: ~
MRAcquisitionType: ~
SliceThickness: ~
FlipAngle: ~
EchoNumbers: ~
EchoTime: ~
RepetitionTime: ~
PhaseEncodingDirection: ~
bids:
acq: gre
rec:
ce:
task:
echo: <EchoNumber>
dir:
run: <AcquisitionNumber>
mod:
suffix: magnitude
- provenance: ~
attributes:
Modality: MR
ProtocolName: ~
SeriesDescription: ~
ImageType: "*P*"
SequenceName: ~
SequenceVariant: ~
ScanningSequence: ~
MRAcquisitionType: ~
SliceThickness: ~
FlipAngle: ~
EchoNumbers: ~
EchoTime: ~
RepetitionTime: ~
PhaseEncodingDirection: ~
bids:
acq: gre
rec:
ce:
task:
echo: <EchoNumber>
dir:
run: <AcquisitionNumber>
mod:
suffix: phase
func: # ----------------------- All functional series --------------------
dwi: # ----------------------- All diffusion series ---------------------
fmap: # ----------------------- All fieldmap series ----------------------
beh: # ----------------------- All behavioural data ---------------------
pet: # ----------------------- All PET series ---------------------------
extra_data: # ----------------------- All extra data ---------------------------
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 ---------------