Merge pull request #1 from anushkab/anushkab

Anushkab

matlabCode/createBIDS_anat_Full_T1w_json.m

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+%% Template Matlab script to create an BIDS compatible sub-01_ses-01_acq-FullExample_run-01_T1w.json file
+% This example lists all required  RECOMMENDED and optional fields.
+% When adding additional metadata please use camelcase
+% 
+%
+% anushkab, 2018
+%%
+clear all
+root_dir = '../';
+project_label = 'templates';
+sub_id = '01';
+ses_id = '01';
+
+%The OPTIONAL “acq-<label>” key/value pair corresponds to a custom label the user MAY use to distinguish a different set of parameters used for acquiring the same modality. 
+
+acq_id = 'FullExample'; 
+
+acquisition = 'anat';
+
+%OPTIONAL “ce-<label>” key/value can be used to distinguish sequences using different contrast enhanced images
+%OPTIONAL “rec-<label>” key/value can be used to distinguish different reconstruction algorithms 
+
+run_id='01';
+
+
+anat_json_name = fullfile(root_dir,project_label,...
+  ['sub-' sub_id],...==
+              ['ses-' ses_id],acquisition,...
+              ['sub-' sub_id ...
+              '_ses-' ses_id ...
+              '_acq-' acq_id ...
+              '_run-' run_id '_T1w.json']);
+
+% Assign the fields in the Matlab structure that can be saved as a json.
+%
+
+%% all REQUIRED /RECOMMENDED /OPTIONAL metadata fields for Magnetic Resonance Imaging data
+
+
+
+
+
+%Scanner Hardware metadata fields
+
+%RECOMMENDED Manufacturer of the equipment that produced the composite instances.
+anat_json.Manufacturer=' ';
+
+%RECOMMENDED Manufacturer`s model name of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1090 “Manufacturers Model Name”.
+anant_json.ManufacturersModelName=' ';
+
+%RECOMMENDED Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018,0087 “Magnetic Field Strength” .
+anat_json.MagneticFieldStrength=' ';
+
+
+%RECOMMENDED The serial number of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1000 ”DeviceSerialNumber”. 
+anat_json.DeviceSerialNumber=' ';
+
+%RECOMMENDED Institution defined name of the machine that produced the composite instances. Corresponds to DICOM Tag 0008, 1010 “Station Name”
+anat_json.StationName= ' '; 
+
+%RECOMMENDED Manufacturer’s designation of software version of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1020 “Software Versions”.
+anat_json.SoftwareVersions= ' ';
+
+%RECOMMENDED (Deprecated) Manufacturer’s designation of the software of the device that created this Hardcopy Image (the printer). Corresponds to DICOM Tag 0018, 101A “Hardcopy Device Software Version”
+anat_json.HardcopyDeviceSoftwareVersion=' ';
+
+%RECOMMENDED  Information describing the receiver coil
+anat_json.ReceiveCoilName= ' ' ;
+
+%RECOMMENDED Information describing the active/selected elements of the receiver coil. 
+anat_json.ReceiveCoilActiveElements=' ';
+
+
+%RECOMMENDED the specifications of the actual gradient coil from the scanner model
+
+anat_json.GradientSetType=' ';
+
+
+%RECOMMENDED This is a relevant field if a non-standard transmit coil is used. Corresponds to DICOM Tag 0018, 9049 “MR Transmit Coil Sequence”.
+anat_json.MRTransmitCoilSequence=' ';
+
+%RECOMMENDED A method for reducing the number of independent channels by combining in analog the signals from multiple coil elements. There are typically different default modes when using un-accelerated or accelerated (e.g. GRAPPA, SENSE) imaging
+anat_json.MatrixCoilMode=' ';
+
+%RECOMMENDED Almost all fMRI studies using phased-array coils use root-sum-of-squares (rSOS) combination, but other methods exist. The image reconstruction is changed by the coil combination method (as for the matrix coil mode above), so anything non-standard should be reported.
+anat_json.CoilCombinationMethod=' ';
+
+
+
+%Sequence Specifics metadata fields
+
+%RECOMMENDED A general description of the pulse sequence used for the scan (i.e. MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI).
+anat_json.PulseSequenceType=' ';
+
+%RECOMMENDED Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 “Sequence Sequence”.
+anat_json.ScanningSequence=' ';
+
+%RECOMMENDED Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 “Sequence Variant”.
+anat_json.SequenceVariant=' ';
+
+%RECOMMENDED Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 “Scan Options”.
+anat_json.ScanOptions=' ';
+
+%RECOMMENDED Manufacturer’s designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 “Sequence Name”.
+anat_json.SequenceName=' ';
+
+
+%RECOMMENDED Information beyond pulse sequence type that identifies the specific pulse sequence used
+anat_json.PulseSequenceDetails=' ';
+
+%RECOMMENDED Boolean stating if the image saved  has been corrected for gradient nonlinearities by the scanner sequence. 
+anat_json.NonlinearGradientCorrection=' ';
+
+
+
+%In-Plane Spatial Encoding metadata fields
+
+%RECOMMENDED The number of RF excitations need to reconstruct a slice or volume. Please mind that  this is not the same as Echo Train Length which denotes the number of lines of k-space collected after an excitation. 
+anat_json.NumberShots=' ';
+
+%RECOMMENDED The parallel imaging (e.g, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice.
+anat_json.ParallelReductionFactorInPlane=' ';
+
+%RECOMMENDED The type of parallel imaging used (e.g. GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 “Parallel Acquisition Technique”. 
+anat_json.ParallelAcquisitionTechnique=' ';
+
+%RECOMMENDED The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 ”Partial Fourier”.
+anat_json.PartialFourier=' ';
+
+%RECOMMENDED The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 “Partial Fourier Direction
+anat_json.PartialFourierDirection=' ';
+
+%REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions
+%PhaseEncodingDirection is defined as the direction along which phase is was modulated which may result in visible distortions.
+anat_json.PhaseEncodingDirection=' ';
+
+
+
+%REQUIRED if corresponding fieldmap data is present. 
+%The “effective” sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction.  
+anat_json.EffectiveEchoSpacing=' ';
+
+
+%REQUIRED if corresponding “field/distortion” maps acquired with opposing phase encoding directions are present
+%This is actually the “effective” total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion.  It is NOT the actual, physical duration of the readout train
+anat_json.TotalReadoutTime=' ';
+
+%RECOMMENDED defined as the displacement of the water signal with respect to fat signal in the image. Water-fat shift (WFS) is expressed in number of pixels 
+anat_json.WaterFatShift=' ';
+
+%RECOMMENDED Number of lines in k-space acquired per excitation per image.
+anat_json.EchoTrainLength=' ';
+
+
+
+%Timing Parameters metadata fields
+
+%REQUIRED if corresponding fieldmap data is present or the data comes from a multi echo sequence
+%The echo time (TE) for the acquisition, specified in seconds. 
+%Corresponds to DICOM Tag 0018, 0081 “Echo Time” 
+anat_json.EchoTime=' ';
+
+
+
+%RECOMMENDED The inversion time (TI) for the acquisition, specified in seconds. Inversion time is the time after the middle of inverting RF pulse to middle of excitation pulse to detect the amount of longitudinal magnetization
+anat_json.InversionTime=' ';
+
+%REQUIRED for sparse sequences that do not have the DelayTime field set. In addition without this parameter slice time correction will not be possible.
+%The time at which each slice was acquired within each volume (frame) of  the acquisition. 
+anat_json.SliceTiming=' ';
+
+
+%RECOMMENDED  Possible values: “i”, “j”, “k”, “i-”, “j-”, “k-” (the axis of the NIfTI data along which slices were acquired, and the direction in which SliceTiming is  defined with respect to). "i", "j", "k" identifiers correspond to the first, second and third axis of the data in the NIfTI file
+%When present ,the axis defined by SliceEncodingDirection  needs to be consistent with the ‘slice_dim’ field in the NIfTI header.
+anat_json.SliceEncodingDirection=' ';
+
+%RECOMMENDED Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling.  For Siemens, this corresponds to DICOM field (0019,1018) (in ns).   
+anat_json.DwellTime=' ';
+
+
+%RF & Contrast metadata field
+
+%RECOMMENDED Flip angle for the acquisition, specified in degrees. Corresponds to: DICOM Tag 0018, 1314 “Flip Angle”.
+anat_json.FlipAngle=' ';
+
+
+%Slice Acceleration metadata field
+
+%RECOMMENDED The multiband factor, for multiband acquisitions.
+anat_json.MultibandAccelerationFactor=' ';
+
+
+%Anatomical landmarks metadata fields
+
+%RECOMMENDED Key:value pairs of any number of additional anatomical landmarks and their coordinates in voxel units
+anat_json.AnatomicalLandmarkCoordinates=' ';
+
+%Institution information metadata fields
+
+
+%RECOMMENDED The name of the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0080 ”InstitutionName”.
+anat_json.InstitutionName=' ';
+
+%RECOMMENDED The address of the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0081 ”InstitutionAddress”
+anat_json.InstitutionAddress=' ';
+
+%RECOMMENDED The department in the  institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1040 ”Institutional Department Name”.
+anat_json.InstitutionalDepartmentName=' ';
+
+
+%OPTIONAL JSON field specific to anatomical scans
+%Active ingredient of agent.  Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.
+anat_json.ContrastBolusIngredient=' ';
+
+
+json_options.indent               = '    '; % this makes the json look pretier when opened in a txt editor
+
+jsonSaveDir = fileparts(anat_json_name);
+if ~isdir(jsonSaveDir)
+    fprintf('Warning: directory to save json file does not exist, create: %s \n',jsonSaveDir)
+end
+
+
+jsonwrite(anat_json_name,anat_json,json_options)
+
+

matlabCode/createBIDS_anat_Short_T1w_json.m

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+%% Template Matlab script to create an BIDS compatible sub-01_ses-01_acq-ShortExample_run-01_T1w.json file
+% This example lists only the required  fields.
+% When adding additional metadata please use camelcase
+% 
+%
+% anushkab, 2018
+%%
+clear all
+root_dir = '../';
+project_label = 'templates';
+sub_id = '01';
+ses_id = '01';
+
+%The OPTIONAL “acq-<label>” key/value pair corresponds to a custom label the user MAY use to distinguish a different set of parameters used for acquiring the same modality. 
+
+acq_id = 'ShortExample'; 
+
+acquisition = 'anat';
+
+%OPTIONAL “ce-<label>” key/value can be used to distinguish sequences using different contrast enhanced images
+%OPTIONAL “rec-<label>” key/value can be used to distinguish different reconstruction algorithms 
+
+run_id='01';
+
+
+anat_json_name = fullfile(root_dir,project_label,...
+  ['sub-' sub_id],...==
+              ['ses-' ses_id],acquisition,...
+              ['sub-' sub_id ...
+              '_ses-' ses_id ...
+              '_acq-' acq_id ...
+              '_run-' run_id '_T1w.json']);
+
+% Assign the fields in the Matlab structure that can be saved as a json.
+%
+
+%% all REQUIRED metadata fields for Magnetic Resonance Imaging data
+
+
+
+
+
+%In-Plane Spatial Encoding metadata fields
+
+
+%REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions
+%PhaseEncodingDirection is defined as the direction along which phase is was modulated which may result in visible distortions.
+anat_json.PhaseEncodingDirection=' ';
+
+
+
+%REQUIRED if corresponding fieldmap data is present. 
+%The “effective” sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction.  
+anat_json.EffectiveEchoSpacing=' ';
+
+
+%REQUIRED if corresponding “field/distortion” maps acquired with opposing phase encoding directions are present
+%This is actually the “effective” total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion.  It is NOT the actual, physical duration of the readout train
+anat_json.TotalReadoutTime=' ';
+
+
+
+
+%Timing Parameters metadata fields
+
+%REQUIRED if corresponding fieldmap data is present or the data comes from a multi echo sequence
+%The echo time (TE) for the acquisition, specified in seconds. 
+%Corresponds to DICOM Tag 0018, 0081 “Echo Time” 
+anat_json.EchoTime=' ';
+
+
+
+%REQUIRED for sparse sequences that do not have the DelayTime field set. In addition without this parameter slice time correction will not be possible.
+%The time at which each slice was acquired within each volume (frame) of  the acquisition. 
+anat_json.SliceTiming=' ';
+
+
+
+
+json_options.indent               = '    '; % this makes the json look pretier when opened in a txt editor
+
+jsonSaveDir = fileparts(anat_json_name);
+if ~isdir(jsonSaveDir)
+    fprintf('Warning: directory to save json file does not exist, create: %s \n',jsonSaveDir)
+end
+
+
+jsonwrite(anat_json_name,anat_json,json_options)
+
+

templates/sub-01/ses-01/anat/sub-01_ses-01_acq-FullExample_run-01_T1w.json

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+{
+    "Manufacturer": " ",
+    "MagneticFieldStrength": " ",
+    "DeviceSerialNumber": " ",
+    "StationName": " ",
+    "SoftwareVersions": " ",
+    "HardcopyDeviceSoftwareVersion": " ",
+    "ReceiveCoilName": " ",
+    "ReceiveCoilActiveElements": " ",
+    "GradientSetType": " ",
+    "MRTransmitCoilSequence": " ",
+    "MatrixCoilMode": " ",
+    "CoilCombinationMethod": " ",
+    "PulseSequenceType": " ",
+    "ScanningSequence": " ",
+    "SequenceVariant": " ",
+    "ScanOptions": " ",
+    "SequenceName": " ",
+    "PulseSequenceDetails": " ",
+    "NonlinearGradientCorrection": " ",
+    "NumberShots": " ",
+    "ParallelReductionFactorInPlane": " ",
+    "ParallelAcquisitionTechnique": " ",
+    "PartialFourier": " ",
+    "PartialFourierDirection": " ",
+    "PhaseEncodingDirection": " ",
+    "EffectiveEchoSpacing": " ",
+    "TotalReadoutTime": " ",
+    "WaterFatShift": " ",
+    "EchoTrainLength": " ",
+    "EchoTime": " ",
+    "InversionTime": " ",
+    "SliceTiming": " ",
+    "SliceEncodingDirection": " ",
+    "DwellTime": " ",
+    "FlipAngle": " ",
+    "MultibandAccelerationFactor": " ",
+    "AnatomicalLandmarkCoordinates": " ",
+    "InstitutionName": " ",
+    "InstitutionAddress": " ",
+    "InstitutionalDepartmentName": " ",
+    "ContrastBolusIngredient": " "
+}

templates/sub-01/ses-01/anat/sub-01_ses-01_acq-ShortExample_run-01_T1w.json

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+{
+    "PhaseEncodingDirection": " ",
+    "EffectiveEchoSpacing": " ",
+    "TotalReadoutTime": " ",
+    "EchoTime": " ",
+    "SliceTiming": " "
+}