Comments (5)
There must be something in your bidsmap.yaml file that I haven't encountered before. Can you send me your organized/code/bidscoin/bidsmap.yaml
file so I can have a look?
from bidscoin.
Hi Marcel,
some background: I want to organize SWI data as anat/T2*.
thanks,
Pim
# --------------------------------------------------------------------------------
# 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:
bidscoin:
version: 3.0.8 # 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: module add 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:
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 runs --------------------
func: # ----------------------- All functional runs --------------------
dwi: # ----------------------- All diffusion runs ---------------------
fmap: # ----------------------- All fieldmap runs ----------------------
beh: # ----------------------- All behavioural data -------------------
pet: # ----------------------- All PET runs ---------------------------
extra_data: # ----------------------- All extra data -------------------------
- provenance: /Users/pimpullens/DATA/currentProjects/HAPCI/swi/DATA/microbleeds/AMC_Anonymous/pt100_mm0/00701_SWIp_fast/00001.dcm
attributes:
Modality: MR
ProtocolName: SWIp_fast SENSE
SeriesDescription: SWIp_fast
ImageType: "['ORIGINAL', 'PRIMARY', 'SW_M_FFE', 'SW_M', 'FFE']"
SequenceName: ''
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '2'
FlipAngle: '17'
EchoNumbers: 1
EchoTime: '0'
RepetitionTime: '31'
PhaseEncodingDirection: ''
bids:
acq: SWIpfast
rec:
ce:
task:
echo: '1'
dir: ROW
run: <<1>>
mod:
suffix:
- provenance: /Users/pimpullens/DATA/currentProjects/HAPCI/swi/DATA/microbleeds/AMC_Anonymous/pt100_mm1/00701_SWIp_fast/00001.dcm
attributes:
Modality: MR
ProtocolName: SWIp_fast
SeriesDescription: SWIp_fast
ImageType: "['ORIGINAL', 'PRIMARY', 'SW_M_FFE', 'SW_M', 'FFE']"
SequenceName: ''
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '2'
FlipAngle: '17'
EchoNumbers: 1
EchoTime: '0'
RepetitionTime: '31'
PhaseEncodingDirection: ''
bids:
acq: SWIpfast
rec:
ce:
task:
echo: '1'
dir: ROW
run: <<1>>
mod:
suffix:
- provenance: /Users/pimpullens/DATA/currentProjects/HAPCI/swi/DATA/microbleeds/AMC_Anonymous/pt108_mm0/00701_SWIp_fast/00001.dcm
attributes:
Modality: MR
ProtocolName: WIP SWIp_fast
SeriesDescription: SWIp_fast
ImageType: "['ORIGINAL', 'PRIMARY', 'SW_M_FFE', 'SW_M', 'FFE']"
SequenceName: ''
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '2'
FlipAngle: '17'
EchoNumbers: 1
EchoTime: '0'
RepetitionTime: '31'
PhaseEncodingDirection: ''
bids:
acq: SWIpfast
rec:
ce:
task:
echo: '1'
dir: ROW
run: <<1>>
mod:
suffix:
- provenance: /Users/pimpullens/DATA/currentProjects/HAPCI/swi/DATA/microbleeds/AMC_Anonymous/pt108_mm0/00702_SWI/00001.dcm
attributes:
Modality: MR
ProtocolName: SWI
SeriesDescription: SWI
ImageType: "['ORIGINAL', 'PRIMARY', 'PROJECTION IMAGE', 'SW_M', 'FFE']"
SequenceName: ''
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '3'
FlipAngle: '17'
EchoNumbers: 1
EchoTime: '0'
RepetitionTime: '31'
PhaseEncodingDirection: ''
bids:
acq: SWI
rec:
ce:
task:
echo: '1'
dir: <InPlanePhaseEncodingDirection>
run: <<1>>
mod:
suffix:
- provenance: /Users/pimpullens/DATA/currentProjects/HAPCI/swi/DATA/microbleeds/AMC_Anonymous/pt44_mm1/00701_SWIp_fast/00001.dcm
attributes:
Modality: MR
ProtocolName: WIP SWIp_fast SENSE
SeriesDescription: SWIp_fast
ImageType: "['ORIGINAL', 'PRIMARY', 'SW_M_FFE', 'SW_M', 'FFE']"
SequenceName: ''
SequenceVariant: SP
ScanningSequence: GR
MRAcquisitionType: 3D
SliceThickness: '2'
FlipAngle: '17'
EchoNumbers: 1
EchoTime: '0'
RepetitionTime: '31'
PhaseEncodingDirection: ''
bids:
acq: SWIpfast
rec:
ce:
task:
echo: '1'
dir: ROW
run: <<1>>
mod:
suffix:
leave_out: # ----------------------- Data that will be left out -------------
PAR:
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 runs --------------------
func: # ----------------------- All functional runs --------------------
dwi: # ----------------------- All diffusion runs ---------------------
fmap: # ----------------------- All fieldmap runs ----------------------
beh: # ----------------------- All behavioural data -------------------
pet: # ----------------------- All PET runs ---------------------------
extra_data: # ----------------------- All extra data -------------------------
leave_out: # ----------------------- Data that will be left out -------------
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:
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 runs --------------------
func: # ----------------------- All functional runs --------------------
dwi: # ----------------------- All diffusion runs ---------------------
fmap: # ----------------------- All fieldmap runs ----------------------
beh: # ----------------------- All behavioural data -------------------
extra_data: # ----------------------- All extra data -------------------------
leave_out: # ----------------------- Data that will be left out -------------
from bidscoin.
Mhhh, I can edit your bidsmap just fine here on my Linux machine. I don't have a Mac to test the GUI, but it could perhaps be that the QTableWidget of the PyQT library doesn't properly read out the mouse position OSX? Do you have the possibility to test this under e.g. Linux?
from bidscoin.
Mhhh, when I upgrade to the latest PyQT5 library I also get some errors. Could you try to run this in your bidscoin python environment and then try again?
pip uninstall pyqt5
pip install pyqt5==5.12.2
from bidscoin.
Fixed with commit a49beb1
from bidscoin.
Related Issues (20)
- bidscoiner with -session option HOT 18
- spec2nii `anon` option does not create de-identified nii/json outputs HOT 5
- Update bidscoin on Neurodesk HOT 2
- Add citation information for plugin tools HOT 6
- Failed to execute bidscoin with 4.2.1 HOT 2
- cannot import name 'files' from 'importlib.resources' HOT 5
- ERROR | Could not parse required sub-<label> label HOT 57
- Using `PhaseEncodingDirection` field to distinguish sequences HOT 6
- Add easy to check output with information on what source was converted to what BIDS files HOT 13
- Derivatives data HOT 4
- Add CSA header support HOT 9
- bidscoiner function leaves out every sequence HOT 65
- Clicking on item in bidsmapper GUI crashes program HOT 1
- Make a bids2bids template bidsmap
- Bidsmap schema doesn't require meta key in plugin HOT 17
- Can path to .bidscoin be configured? HOT 62
- B0FieldSource as a list HOT 12
- Exclude sections behaves weirdly HOT 53
- IndexError: string index out of range in dcm2niix2bids.py HOT 6
- New BIDS feature of dcm2niix HOT 2
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