From 8046a2fec8489256978f44a8bb8adbcc35fef7f6 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 14:50:51 +0100 Subject: [PATCH] fix --- .../magnetic-resonance-imaging-data.md | 552 ++++++------------ 1 file changed, 182 insertions(+), 370 deletions(-) diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md index a2a39b06c4..de45eb194a 100644 --- a/src/modality-specific-files/magnetic-resonance-imaging-data.md +++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md @@ -2,16 +2,9 @@ ## Common metadata fields -MR Data described in the following sections share the following RECOMMENDED metadata -fields (stored in sidecar JSON files). -MRI acquisition parameters are divided into several categories based on -"A checklist for fMRI acquisition methods reporting in the literature" -([article](https://doi.org/10.15200/winn.143191.17127)) by Ben Inglis. +MR Data described in the following sections share the following RECOMMENDED metadata fields (stored in sidecar JSON files). MRI acquisition parameters are divided into several categories based on "A checklist for fMRI acquisition methods reporting in the literature" ([article](https://doi.org/10.15200/winn.143191.17127)) by Ben Inglis. -When adding additional metadata please use the CamelCase version of -[DICOM ontology terms](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_d.html) -whenever possible. See also -[recommendations on JSON files](../common-principles.md#key-value-files-dictionaries). +When adding additional metadata please use the CamelCase version of [DICOM ontology terms](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_d.html) whenever possible. See also [recommendations on JSON files](../common-principles.md#key-value-files-dictionaries). ### Hardware information @@ -23,22 +16,12 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table("mri.MRIHardware") }} Example for `ReceiveCoilActiveElements`: -For Siemens, coil channels are typically not activated/selected individually, -but rather in pre-defined selectable "groups" of individual channels, -and the list of the "groups" of elements that are active/selected in any -given scan populates the `Coil String` entry in Siemens' private DICOM fields -(for example, `HEA;HEP` for the Siemens standard 32 ch coil -when both the anterior and posterior groups are activated). -This is a flexible field that can be used as most appropriate for a given -vendor and coil to define the "active" coil elements. -Since individual scans can sometimes not have the intended coil elements selected, -it is preferable for this field to be populated directly from the DICOM -for each individual scan, so that it can be used as a mechanism for checking -that a given scan was collected with the intended coil elements selected. +For Siemens, coil channels are typically not activated/selected individually, but rather in pre-defined selectable "groups" of individual channels, and the list of the "groups" of elements that are active/selected in any given scan populates the `Coil String` entry in Siemens' private DICOM fields (for example, `HEA;HEP` for the Siemens standard 32 ch coil when both the anterior and posterior groups are activated). This is a flexible field that can be used as most appropriate for a given vendor and coil to define the "active" coil elements. Since individual scans can sometimes not have the intended coil elements selected, it is preferable for this field to be populated directly from the DICOM for each individual scan, so that it can be used as a mechanism for checking that a given scan was collected with the intended coil elements selected. ### Institution information @@ -50,6 +33,7 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table("mri.MRIInstitutionInformation") }} ### Sequence Specifics @@ -62,6 +46,7 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table("mri.MRISequenceSpecifics") }} ### In- and Out-of-Plane Spatial Encoding @@ -74,19 +59,12 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table(["mri.MRISpatialEncoding", "mri.PhaseEncodingDirectionRec"]) }} -2Conveniently, for Siemens data, this value is easily obtained as -`1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the -"BandwidthPerPixelPhaseEncode" in DICOM Tag 0019, 1028 and ReconMatrixPE is -the size of the actual reconstructed data in the phase direction (which is NOT -reflected in a single DICOM Tag for all possible aforementioned scan -manipulations). See -[Acquiring and using field maps - LCNI](https://lcni.uoregon.edu/wiki/acquiring-and-using-field-maps/) -and [TotalReadoutTime - dcm\_qa](https://github.com/neurolabusc/dcm_qa/tree/master/In/TotalReadoutTime). +2Conveniently, for Siemens data, this value is easily obtained as `1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the "BandwidthPerPixelPhaseEncode" in DICOM Tag 0019, 1028 and ReconMatrixPE is the size of the actual reconstructed data in the phase direction (which is NOT reflected in a single DICOM Tag for all possible aforementioned scan manipulations). See [Acquiring and using field maps - LCNI](https://lcni.uoregon.edu/wiki/acquiring-and-using-field-maps/) and [TotalReadoutTime - dcm_qa](https://github.com/neurolabusc/dcm_qa/tree/master/In/TotalReadoutTime). -3We use the time between the center of the first "effective" echo -and the center of the last "effective" echo, sometimes called the "FSL definition". +3We use the time between the center of the first "effective" echo and the center of the last "effective" echo, sometimes called the "FSL definition". ### Timing Parameters @@ -98,6 +76,7 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table(["mri.MRITimingParameters", "mri.SliceTimingMRI"]) }} ### RF & Contrast @@ -110,6 +89,7 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table(["mri.MRIFlipAngleLookLockerFalse", "mri.MRIRFandContrast" ]) }} ### Slice Acceleration @@ -122,6 +102,7 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table("mri.MRISliceAcceleration") }} ### Anatomical landmarks @@ -136,21 +117,14 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table("mri.MRIAnatomicalLandmarks") }} -### Echo-Planar Imaging and *B0* mapping +### Echo-Planar Imaging and _B0_ mapping -Echo-Planar Imaging (EPI) schemes typically used in the acquisition of -diffusion and functional MRI may also be *intended for* estimating the -*B0* field nonuniformity inside the scanner (in other words, -*mapping the field*) without the acquisition of additional MRI schemes -such as gradient-recalled echo (GRE) sequences that are stored under the -`fmap/` directory of the BIDS structure. +Echo-Planar Imaging (EPI) schemes typically used in the acquisition of diffusion and functional MRI may also be _intended for_ estimating the _B0_ field nonuniformity inside the scanner (in other words, _mapping the field_) without the acquisition of additional MRI schemes such as gradient-recalled echo (GRE) sequences that are stored under the `fmap/` directory of the BIDS structure. -The modality labels `dwi` (under `dwi/`), `bold` (under `func/`), -`asl` (under `perf/`), `sbref` (under `dwi/`, `func/` or `perf/`), and -any modality under `fmap/` are allowed to encode the MR protocol intent for -fieldmap estimation using the following metadata: +The modality labels `dwi` (under `dwi/`), `bold` (under `func/`), `asl` (under `perf/`), `sbref` (under `dwi/`, `func/` or `perf/`), and any modality under `fmap/` are allowed to encode the MR protocol intent for fieldmap estimation using the following metadata: + {{ MACROS___make_sidecar_table([ "mri.MRIB0FieldIdentifier", "mri.MRIEchoPlanarImagingAndB0FieldSource", @@ -176,12 +151,12 @@ The definitions of the fields specified in these tables may be found in A guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_sidecar_table("mri.MRISample") }} ### Deidentification information -Describes the mechanism or method used to modify or remove metadata -and/or pixel data to protect the patient or participant's identity. +Describes the mechanism or method used to modify or remove metadata and/or pixel data to protect the patient or participant's identity. + {{ MACROS___make_sidecar_table("mri.DeidentificationMethod") }} Each object in the `DeidentificationMethodCodeSequence` array includes the following RECOMMENDED keys: @@ -201,21 +177,18 @@ The definitions of these fields can be found in and a guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_subobject_table("metadata.DeidentificationMethodCodeSequence.items") }} ## Anatomy imaging data Anatomy MRI sequences measure static, structural features of the brain. -This datatype is divided into two groups: -non-parametric and parametric. +This datatype is divided into two groups: non-parametric and parametric. -Non-parametric structural images have an arbitrary scale. -For example, T1w data are T1-weighted, -but the values do not correspond to actual T1 value estimates. +Non-parametric structural images have an arbitrary scale. For example, T1w data are T1-weighted, but the values do not correspond to actual T1 value estimates. -Parametric structural imaging, on the other hand, use a non-arbitrary scale. -For example, a T1map file contains T1 value estimates, in seconds. +Parametric structural imaging, on the other hand, use a non-arbitrary scale. For example, a T1map file contains T1 value estimates, in seconds. ### Non-parametric structural MR images @@ -226,6 +199,7 @@ The inputs for this macro can be found in the directory and a guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_filename_template("raw", datatypes=["anat"], suffixes=[ "T1w", "T2w", @@ -249,6 +223,7 @@ The definitions of these fields can be found in and a guide for using macros can be found at https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md --> + {{ MACROS___make_suffix_table( [ "T1w", @@ -265,19 +240,13 @@ and a guide for using macros can be found at ) }} -The [`part-