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annotate Sphinx/source/users/anonymization.rst @ 247:325dd3901547
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Sun, 19 May 2019 10:08:52 +0200 |
| parents | 02399e86f046 |
| children | 829ce317d215 |
| rev | line source |
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| 0 | 1 .. highlight:: bash |
| 2 .. _anonymization: | |
| 3 | |
| 4 Anonymization and modification | |
| 5 ============================== | |
| 6 | |
| 7 .. contents:: | |
| 8 :depth: 2 | |
| 9 | |
| 10 Orthanc 0.5.0 introduces the anonymization of DICOM resources | |
| 11 (i.e. patients, studies, series or instances). This page summarizes | |
| 12 how to use this feature. | |
| 13 | |
| 14 | |
| 15 Anonymization of a Single Instance | |
| 16 ---------------------------------- | |
| 17 | |
| 18 Orthanc allows to anonymize a single DICOM instance and to download | |
| 19 the resulting anonymized DICOM file. Anonymization consists in erasing | |
| 20 all the tags that are specified in Table E.1-1 from PS 3.15 of the | |
| 111 | 21 DICOM standard 2008 or 2017c (default). Example:: |
| 0 | 22 |
| 23 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{}' > Anonymized.dcm | |
| 24 | |
| 25 It is possible to control how anonymization is achieved by specifying | |
| 26 a JSON body:: | |
| 27 | |
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28 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{"Replace":{"PatientName":"Hello","0010-1001":"World"},"Keep":["StudyDescription", "SeriesDescription"],"KeepPrivateTags": true, "DicomVersion" : "2017c"}' > Anonymized.dcm |
| 0 | 29 |
| 30 Explanations: | |
| 31 | |
| 32 * New UUIDs are automatically generated for the study, the series and | |
| 33 the instance. | |
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34 * The DICOM tags can be specified either by their name |
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35 (``PatientName``) or by their hexadecimal identifier (in the example |
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36 above, ``0010-1001`` corresponds to ``Other Patient Names``). |
| 0 | 37 * ``Replace`` is an associative array that associates a DICOM tag with its |
| 38 new string value. The value is dynamically cast to the proper DICOM | |
| 39 data type (an HTTP error will occur if the cast fails). Replacements | |
| 40 are applied after all the tags to anonymize have been removed. | |
| 41 * ``Keep`` specifies a list of tags that should be preserved from full | |
| 42 anonymization. | |
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43 * If ``KeepPrivateTags`` is set to ``true`` in the JSON request, |
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44 private tags (i.e. manufacturer-specific tags) are not removed by |
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45 the anonymization process. The default behavior consists in removing |
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46 the private tags, as such tags can contain patient-specific |
| 0 | 47 information. |
| 111 | 48 * ``DicomVersion`` specifies which version of the DICOM standard shall be used |
| 49 for anonymization. Allowed values are ``2008`` and ``2017c`` (default value | |
| 50 if the parameter is absent). This parameter has been introduced in Orthanc | |
| 51 1.3.0. In earlier version, the ``2008`` standard was used. | |
| 0 | 52 |
| 53 | |
| 54 Modification of a Single Instance | |
| 55 --------------------------------- | |
| 56 | |
| 57 Orthanc allows to modify a set of specified tags in a single DICOM | |
| 58 instance and to download the resulting anonymized DICOM | |
| 59 file. Example:: | |
| 60 | |
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61 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/modify -X POST -d '{"Replace":{"PatientName":"hello","PatientID":"world"},"Remove":["InstitutionName"],"RemovePrivateTags": true, "Force": true}' > Modified.dcm |
| 0 | 62 |
| 63 Remarks: | |
| 64 | |
| 65 * The ``Remove`` array specifies the list of the tags to remove. | |
| 66 * The ``Replace`` associative array specifies the substitions to be applied (cf. anonymization). | |
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67 * If ``RemovePrivateTags`` is set to ``true``, the private tags |
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68 (i.e. manufacturer-specific tags) are removed. |
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69 * The ``Force`` option must be set to ``true``, in order to allow the |
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70 modification of the ``PatientID``, as such a modification of the |
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71 :ref:`DICOM identifiers <dicom-identifiers>` might lead to breaking |
| 113 | 72 the DICOM model of the real-world. In general, any explicit |
| 73 modification to one of the ``PatientID``, ``StudyInstanceUID``, | |
| 74 ``SeriesInstanceUID``, and ``SOPInstanceUID`` requires ``Force`` to | |
| 75 be set to ``true``, in order to prevent any unwanted side effect. | |
| 0 | 76 |
| 77 | |
| 78 Modification of Studies or Series | |
| 79 --------------------------------- | |
| 80 | |
| 81 .. highlight:: bash | |
| 82 | |
| 83 It is possible to modify all the instances from a study or from a | |
| 84 series in a single request. In this case, the modified instances are | |
| 85 stored back into the Orthanc store. Here is how to modify a series:: | |
| 86 | |
| 87 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
| 88 | |
| 89 | |
| 90 .. highlight:: json | |
| 91 | |
| 92 The parameters are identical to those used to modify a single | |
| 93 instance. Orthanc will answer a JSON message that tells where the | |
| 94 modified series has been stored:: | |
| 95 | |
| 96 { | |
| 97 "ID" : "3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce", | |
| 98 "Path" : "/series/3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce" | |
| 99 } | |
| 100 | |
| 101 | |
| 102 .. highlight:: bash | |
| 103 | |
| 104 Similarly, here is an interaction to modify a study:: | |
| 105 | |
| 106 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
| 107 | |
| 108 .. highlight:: json | |
| 109 | |
| 110 :: | |
| 111 | |
| 112 { | |
| 113 "ID" : "1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28", | |
| 114 "Path" : "/studies/1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28" | |
| 115 } | |
| 116 | |
| 117 | |
| 118 Modification of Patients | |
| 119 ------------------------ | |
| 120 | |
| 121 .. highlight:: bash | |
| 122 | |
| 123 Starting with Orthanc 0.7.5, Orthanc can also modify all the instances | |
| 124 of a patient with a single REST call. Here is a sample:: | |
| 125 | |
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126 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/modify -X POST -d '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}' |
| 0 | 127 |
| 128 .. highlight:: json | |
| 129 | |
| 130 :: | |
| 131 | |
| 132 { | |
| 133 "ID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 134 "Path" : "/patients/f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 135 "PatientID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
| 136 "Type" : "Patient" | |
| 137 } | |
| 138 | |
| 139 Please note that, in this case, you have to set the value of the | |
| 140 ``PatientID (0010,0020)`` tag for Orthanc to accept this modification: | |
| 141 This is a security to prevent the merging of patient data before and | |
| 142 after anonymization, if the user does not explicitly tell Orthanc to | |
| 143 do so. | |
| 144 | |
| 145 | |
| 146 Anonymization of Patients, Studies or Series | |
| 147 -------------------------------------------- | |
| 148 | |
| 149 .. highlight:: bash | |
| 150 | |
| 151 Study and series can be anonymized the same way as they are modified:: | |
| 152 | |
| 153 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/anonymize -X POST -d '{}' | |
| 154 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/anonymize -X POST -d '{}' | |
| 155 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/anonymize -X POST -d '{}' | |
| 156 | |
| 157 As written above, the anonymization process can be fine-tuned by using | |
| 158 a JSON body. | |
| 167 | 159 |
| 160 | |
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161 .. _split-merge: |
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162 |
| 167 | 163 Split/merge of DICOM studies |
| 164 ---------------------------- | |
| 165 | |
| 178 | 166 Starting with Orthanc 1.5.0, Orthanc supports splitting and merging |
| 167 | 167 DICOM studies through its REST API. |
| 168 | |
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169 .. _split: |
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170 |
| 167 | 171 Splitting |
| 172 ^^^^^^^^^ | |
| 173 | |
| 174 Here is the syntax to **split** a DICOM study:: | |
| 175 | |
| 176 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/split -d \ | |
| 177 '{"Series":["6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"],"Replace":{"PatientName":"HELLO"},"Remove":["AccessionNumber"]}' | |
| 178 | |
| 179 By issuing this command, the series whose :ref:`Orthanc identifier | |
| 180 <dicom-identifiers>` is | |
| 181 ``6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228``, and that is part of | |
| 182 the source study with identifier | |
| 183 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``, will be removed from | |
| 184 the source study, and will be moved to a brand new study. | |
| 185 | |
| 186 This is done by generating a new value for all the following DICOM | |
| 187 tags in the DICOM instances of the series of interest: | |
| 188 ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID (0x0020, | |
| 189 0x000e)``, and ``SOPInstanceUID (0x0008, 0x0018)``. Here are the | |
| 190 arguments of this ``/studies/{study}/split`` URI: | |
| 191 | |
| 192 * ``Series`` gives the list of series to be separated from the parent | |
| 193 study (mandatory option). These series must all be children of the | |
| 194 same source study, that is specified in the URI. | |
| 195 * ``Replace`` allows to overwrite the DICOM tags that are part of the | |
| 196 "Patient Module Attributes" and the "General Study Module | |
| 197 Attributes", as specified by the DICOM 2011 standard in Tables C.7-1 | |
| 198 and C.7-3. | |
| 199 * ``Remove`` allows to remove DICOM tags from the same modules as in | |
| 200 the ``Replace`` options. | |
| 201 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
| 202 Orthanc to keep a copy of the original series in the source study. | |
| 203 By default, the original series are deleted from Orthanc. | |
| 204 | |
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205 .. _merge: |
| 167 | 206 |
| 207 Merging | |
| 208 ^^^^^^^ | |
| 209 | |
| 210 Here is the syntax to **merge** DICOM series, into another DICOM study:: | |
| 211 | |
| 212 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/merge -d \ | |
| 213 '{"Resources":["ef2ce55f-9342856a-aee23907-2667e859-9f3b734d"]}' | |
| 214 | |
| 215 By issuing this command, the DICOM series whose :ref:`Orthanc | |
| 216 identifier <dicom-identifiers>` is | |
| 217 ``ef2ce55f-9342856a-aee23907-2667e859-9f3b734d``, will be merged into | |
| 218 target study with identifier | |
| 219 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``. | |
| 220 | |
| 221 As in the case of splitting, this is done by updating the following | |
| 222 DICOM tags: ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID | |
| 223 (0x0020, 0x000e)``, and ``SOPInstanceUID (0x0008, | |
| 224 0x0018)``. Furthermore, all the DICOM tags that are part of the | |
| 225 "Patient Module Attributes" and the "General Study Module Attributes" | |
| 226 (as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3), | |
| 227 are modified to match the target study. Here are the | |
| 228 arguments of this ``/studies/{study}/merge`` URI: | |
| 229 | |
| 230 * ``Resources`` gives the list of source studies or source series | |
| 231 that are to be merged into the target study. | |
| 232 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
| 233 Orthanc to keep the source studies and series. By default, the | |
| 234 original resources are deleted from Orthanc. |