[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET #1772

CGSchwarzMayo · 2024-04-12T14:49:27Z

Add tags for DeIdentificationMethod and DeIdentificationMethodCodeSeuence, corresponding to the same-named DICOM tags. These record info on de-identification, including metadata and image content (e.g. de-facing or removing burned-in text)

…uence, corresponding to the same-named DICOM tags. These record info on de-identification, including metadata and image content (e.g. de-facing or removing burned-in text)

CGSchwarzMayo · 2024-04-12T14:52:54Z

This addresses issue #1709

codecov · 2024-04-12T14:56:22Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 87.93%. Comparing base (01025da) to head (9a32e88).

❗ Current head 9a32e88 differs from pull request most recent head 4fab2f4. Consider uploading reports for the commit 4fab2f4 to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1772   +/-   ##
=======================================
  Coverage   87.92%   87.93%           
=======================================
  Files          16       16           
  Lines        1375     1351   -24     
=======================================
- Hits         1209     1188   -21     
+ Misses        166      163    -3

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

…ethod, to match DICOM

effigies

Okay, to validate these, we will need to add them to sidecars.

https://github.com/bids-standard/bids-specification/blob/master/src/schema/rules/sidecars/mri.yaml

I would suggest a pair of new tables, such as:

DeidentificationMethod:
  selectors:
    - intersects([modality], ["mri", "pet"])
  fields:
    DeidentificationMethod: optional
    DeidentificationMethodCodeSequence:
      level: optional, but recommended if DeidentificationMethod is present

DeidentificationMethodRec:
  selectors:
    - intersects([modality], ["mri", "pet"])
    - sidecar.DeidentificationMethod
  fields:
    DeidentificationMethodCodeSequence: recommended

Then for rendering, these can then be added to the lists of tables for MRI data:

bids-specification/src/modality-specific-files/magnetic-resonance-imaging-data.md

Lines 16 to 176 in d7b3793

    
           ### Hardware information 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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. 
        
           ### Institution information 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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"]) }} 
        
           <sup>2</sup>Conveniently, 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). 
        
           <sup>3</sup>We 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 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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 
        
           Useful for multimodal co-registration with MEG, (S)EEG, TMS, and so on. 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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 *B<sub>0</sub>* mapping 
        
           Echo-Planar Imaging (EPI) schemes typically used in the acquisition of 
        
           diffusion and functional MRI may also be *intended for* estimating the 
        
           *B<sub>0</sub>* 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: 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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.MRIEchoPlanarImagingAndB0Mapping") }} 
        
           #### Tissue description 
        
           <!-- This block generates a metadata table. 
        
           These tables are defined in 
        
             src/schema/rules/sidecars 
        
           The definitions of the fields specified in these tables may be found in 
        
             src/schema/objects/metadata.yaml 
        
           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") }}

e.g.

### Deidentification information

<!-- This block generates a metadata table.
These tables are defined in
  src/schema/rules/sidecars
The definitions of the fields specified in these tables may be found in
  src/schema/objects/metadata.yaml
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.DeidentificationMethod") }}

Each object in the `DeidentificationMethodCodeSequence` array includes the following RECOMMENDED keys:

<!-- This block generates a table describing subfields within a metadata field.
The definitions of these fields can be found in
  src/schema/objects/metadata.yaml
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") }}

And we should do the same for PET.

src/schema/objects/metadata.yaml

CGSchwarzMayo · 2024-04-18T18:21:13Z

I apologize for missing some pieces, and I think I understand, now. Thank you for your careful review and for helping me through this process. I will execute your suggestions and amend the PR with another commit.

effigies · 2024-04-19T20:23:33Z

No need to apologize! I appreciate the effort you're putting into this.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

for more information, see https://pre-commit.ci

CGSchwarzMayo · 2024-04-23T14:34:12Z

Chris,

I committed your suggested diffs as-is. For the tables and sidecars, I deviated a bit in calling both tags optional. My read of DICOM is that if PatientIdentityRemoved is TRUE (which is a tag we don't have in BIDS, and I don't think BIDS really needs it), then at least one of either DeidentificationMethod or DeidentificationCodeSequence is required. Without PatientIdentityRemoved, I would say neither is required, and both are optional. It's not that DeidentificationMethod is recommended if DeidentificationCodeSequence is present, but rather they are of equal status and people can use either. DeidentificationMethod is a single simple string, but there's a greater chance that some downstream software would replace rather than amend the string. DeidentificationCodeSequence better accounts for there being a series of de-identification steps and other software would more likely amend than overwrite it, but it's also a sequence tag and those are unpleasantly messy.

While I was copying from the MRI to the PET table, I noticed the "defacemask" block in the MRI but not PET. I copied this to the PET, since de-facing is also routinely applied to PET now.

I looked for CT-related files, but it appears that CT is not a part of BIDS currently? If CT is ever added, my recommendation is that these elements all be added to CT to match MRI and PET.

Thanks for your help and careful review!

src/modality-specific-files/positron-emission-tomography.md

effigies · 2024-04-23T17:28:18Z

For the tables and sidecars, I deviated a bit in calling both tags optional. My read of DICOM is that if PatientIdentityRemoved is TRUE (which is a tag we don't have in BIDS, and I don't think BIDS really needs it), then at least one of either DeidentificationMethod or DeidentificationCodeSequence is required. Without PatientIdentityRemoved, I would say neither is required, and both are optional.

Sounds good.

While I was copying from the MRI to the PET table, I noticed the "defacemask" block in the MRI but not PET. I copied this to the PET, since de-facing is also routinely applied to PET now.

Could you split that out into a separate PR? I think it will need some additional work to apply properly to PET, and I'd rather not complicate this PR more than necessary.

I looked for CT-related files, but it appears that CT is not a part of BIDS currently? If CT is ever added, my recommendation is that these elements all be added to CT to match MRI and PET.

Correct, and agreed!

effigies

A few small suggestions. Also, in case you haven't seen it hiding in the review boxes (see image), here's the rendered specification, which will update a few minutes after you make pushes to this PR.

src/modality-specific-files/magnetic-resonance-imaging-data.md

src/modality-specific-files/positron-emission-tomography.md

src/schema/rules/sidecars/pet.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

for more information, see https://pre-commit.ci

CGSchwarzMayo · 2024-04-24T20:21:31Z

Chris,
I attempted to make all the changes you suggested. The automated checks that failed appear to be related to parts of the code that I did not change in this branch, so unrelated to my changes. Thanks for your continuing reviews.
Chris

effigies

I'm happy with this from a schema and rendering perspective, and I believe this should be relatively simple to implement for DICOM converters.

I would appreciate if at least a couple representatives of converters could weigh in:

(I know you're all busy, please feel free to delegate.)

For those who would rather read spec than schema:

CGSchwarzMayo · 2024-04-25T13:43:27Z

Thanks Chris (Markiewicz)!

I have a companion PR for dcm2niix at rordenlab/dcm2niix#813, but Chris (Rorden) hasn't commented on it yet. I had initially asked him to add the tags to dcm2niix's .json, and he said to get them added to bids-specification first, so that's how I arrived here.

I don't have any involvement with the other converters.

Thanks,
Chris (Schwarz)

yarikoptic · 2024-04-25T16:10:24Z

src/schema/objects/metadata.yaml

+        type: string
+        description: |
+          An identifier of the version of the coding scheme if necessary to resolve ambiguity.
+          Corresponds to DICOM Tag 0008, 0103 `Coding Scheme Version`.


I think this is complicated enough warranting addition to https://github.com/bids-standard/bids-examples if not as an example here in the BIDS spec text. Do we have some nice example DICOMs to check those fields out?

I think if someone were creating these tags from scratch at the BIDS level, they would use DeidentificationMethod rather than DeidentificationMethodCodeSequence. The latter is more provided to allow direct translation by dcm->nii and dcm->bids software.

I'm attaching some nice example DICOM, as requested. This is MRI of a spaghetti squash (thanks @captainnova), and I've further de-identified it, so there's no PHI. I included the tags as if I had de-faced it, but it is a squash, so there was no face to de-face.

dcm_fruit_deidentified.zip

The relevant dcm tags look like this:

(0012, 0063) De-identification Method LO: ['mri_reface 0.3.4', 'Per DICOM PS 3.15 AnnexE. Details in 0012,0064'] (0012, 0064) De-identification Method Code Sequence 5 item(s) ---- (0008, 0100) Code Value SH: '113102' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0103) Coding Scheme Version SH: '01' (0008, 0104) Code Meaning LO: 'Clean Recognizable Visual Features Option' --------- (0008, 0100) Code Value SH: 'replace_recognizable' (0008, 0102) Coding Scheme Designator SH: 'mri_reface' (0008, 0103) Coding Scheme Version SH: '0.3.4' (0008, 0104) Code Meaning LO: 'Replace face, ears, and artifacts in air' --------- (0008, 0100) Code Value SH: '113100' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0104) Code Meaning LO: 'Basic Application Confidentiality Profile' --------- (0008, 0100) Code Value SH: '113107' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0104) Code Meaning LO: 'Retain Longitudinal Temporal Information Modified Dates Option' --------- (0008, 0100) Code Value SH: '113111' (0008, 0102) Coding Scheme Designator SH: 'DCM' (0008, 0104) Code Meaning LO: 'Retain Safe Private Option' ---------

With rordenlab/dcm2niix#813, the relevant portion of json output is:

"DeidentificationMethod": "mri_reface 0.3.4\\Per DICOM PS 3.15 AnnexE. Details in 0012,0064", "DeidentificationMethodCodeSequence": [ { "CodeValue": "113102", "CodingSchemeDesignator": "DCM", "CodingSchemeVersion": "01", "CodeMeaning": "Clean Recognizable Visual Features Option" }, { "CodeValue": "replace_recognizable", "CodingSchemeDesignator": "mri_reface", "CodingSchemeVersion": "0.3.4", "CodeMeaning": "Replace face, ears, and artifacts in air" }, { "CodeValue": "113100", "CodingSchemeDesignator": "DCM", "CodeMeaning": "Basic Application Confidentiality Profile" }, { "CodeValue": "113107", "CodingSchemeDesignator": "DCM", "CodeMeaning": "Retain Longitudinal Temporal Information Modified Dates Option" }, { "CodeValue": "113111", "CodingSchemeDesignator": "DCM", "CodeMeaning": "Retain Safe Private Option" } ],

Add tags for DeIdentificationMethod and DeIdentificationMethodCodeSeq…

62d2244

…uence, corresponding to the same-named DICOM tags. These record info on de-identification, including metadata and image content (e.g. de-facing or removing burned-in text)

CGSchwarzMayo requested review from tsalo and erdalkaraca as code owners April 12, 2024 14:49

Merge branch 'master' into DeIdentificationMethod

9a32e88

CGSchwarzMayo mentioned this pull request Apr 12, 2024

Annotate MR/PET (+CT) images with deidentification methods #1709

Open

CGSchwarzMayo added 2 commits April 16, 2024 10:51

Correct capitalization on DeIdentificationMethod to DeidentificationM…

c5a7e5c

…ethod, to match DICOM

Merge branch 'master' into DeIdentificationMethod

1589e22

This was referenced Apr 17, 2024

Add DeidentificationMethod and DeidentificationMethodCodeSequence to json rordenlab/dcm2niix#812

Closed

Add DeidentificationMethod and DeidentificationMethodCodeSequence to json rordenlab/dcm2niix#813

Open

effigies reviewed Apr 18, 2024

View reviewed changes

src/schema/objects/metadata.yaml Outdated Show resolved Hide resolved

src/schema/objects/metadata.yaml Outdated Show resolved Hide resolved

CGSchwarzMayo and others added 4 commits April 23, 2024 08:24

Merge branch 'bids-standard:master' into DeIdentificationMethod

4fab2f4

Apply suggestions from code review

a53ab03

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Add modality-specific-files and sidecars for DeidentificationMethod tags

4327bc7

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

edd7448

for more information, see https://pre-commit.ci

effigies reviewed Apr 23, 2024

View reviewed changes

src/modality-specific-files/positron-emission-tomography.md Outdated Show resolved Hide resolved

Update src/modality-specific-files/positron-emission-tomography.md

85c9e80

effigies reviewed Apr 23, 2024

View reviewed changes

src/modality-specific-files/magnetic-resonance-imaging-data.md Outdated Show resolved Hide resolved

src/modality-specific-files/positron-emission-tomography.md Outdated Show resolved Hide resolved

src/schema/rules/sidecars/pet.yaml Outdated Show resolved Hide resolved

CGSchwarzMayo and others added 3 commits April 24, 2024 15:07

Apply additional suggestions from code review

2c01417

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

450b257

for more information, see https://pre-commit.ci

Merge branch 'master' into DeIdentificationMethod

586e839

effigies added 2 commits April 24, 2024 16:34

Fix header levels

5059935

Move deid section under PET metadata

1b3f97c

effigies changed the title ~~[ENH][SCHEMA] Add tags for DeIdentificationMethod/CodeSequence~~ [ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET Apr 24, 2024

effigies approved these changes Apr 24, 2024

View reviewed changes

effigies added the needs review label Apr 24, 2024

yarikoptic reviewed Apr 25, 2024

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET #1772

[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET #1772

CGSchwarzMayo commented Apr 12, 2024

CGSchwarzMayo commented Apr 12, 2024

codecov bot commented Apr 12, 2024 •

edited

effigies left a comment

CGSchwarzMayo commented Apr 18, 2024

effigies commented Apr 19, 2024

CGSchwarzMayo commented Apr 23, 2024

effigies commented Apr 23, 2024

effigies left a comment

CGSchwarzMayo commented Apr 24, 2024

effigies left a comment

CGSchwarzMayo commented Apr 25, 2024 •

edited

yarikoptic Apr 25, 2024

CGSchwarzMayo Apr 25, 2024

	### Hardware information

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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.

	### Institution information

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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"]) }}

	<sup>2</sup>Conveniently, 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).

	<sup>3</sup>We 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

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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

	Useful for multimodal co-registration with MEG, (S)EEG, TMS, and so on.

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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 B<sub>0</sub> mapping

	Echo-Planar Imaging (EPI) schemes typically used in the acquisition of
	diffusion and functional MRI may also be intended for estimating the
	B<sub>0</sub> 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:

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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.MRIEchoPlanarImagingAndB0Mapping") }}

	#### Tissue description

	<!-- This block generates a metadata table.
	These tables are defined in
	src/schema/rules/sidecars
	The definitions of the fields specified in these tables may be found in
	src/schema/objects/metadata.yaml
	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") }}

[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET #1772

Are you sure you want to change the base?

[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET #1772

Conversation

CGSchwarzMayo commented Apr 12, 2024

CGSchwarzMayo commented Apr 12, 2024

codecov bot commented Apr 12, 2024 • edited

Codecov Report

effigies left a comment

Choose a reason for hiding this comment

CGSchwarzMayo commented Apr 18, 2024

effigies commented Apr 19, 2024

CGSchwarzMayo commented Apr 23, 2024

effigies commented Apr 23, 2024

effigies left a comment

Choose a reason for hiding this comment

CGSchwarzMayo commented Apr 24, 2024

effigies left a comment

Choose a reason for hiding this comment

CGSchwarzMayo commented Apr 25, 2024 • edited

yarikoptic Apr 25, 2024

Choose a reason for hiding this comment

CGSchwarzMayo Apr 25, 2024

Choose a reason for hiding this comment

codecov bot commented Apr 12, 2024 •

edited

CGSchwarzMayo commented Apr 25, 2024 •

edited