Mercurial > hg > orthanc-book
annotate Sphinx/source/users/anonymization.rst @ 763:4e9dc26a5cb9 Orthanc-1.9.7
Orthanc 1.9.7
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 31 Aug 2021 11:24:43 +0200 |
parents | 97e6a0431c5e |
children | 01fa632daae9 |
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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 | |
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19 the resulting anonymized DICOM file (without storing the anonymized |
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20 DICOM instance into Orthanc). Anonymization consists in erasing all |
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21 the tags that are specified in `Table E.1-1 from PS 3.15 |
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22 <http://dicom.nema.org/medical/dicom/current/output/chtml/part15/chapter_E.html#table_E.1-1>`__ |
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23 of the DICOM standard 2008, 2017c or 2021b (default). Example:: |
0 | 24 |
25 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{}' > Anonymized.dcm | |
26 | |
27 It is possible to control how anonymization is achieved by specifying | |
28 a JSON body:: | |
29 | |
444 | 30 $ curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST \ |
31 --data '{ | |
32 "Replace": { | |
33 "PatientName": "Hello", | |
34 "0010-1001": "World" | |
35 }, | |
36 "Keep": [ | |
37 "StudyDescription", | |
38 "SeriesDescription" | |
39 ], | |
40 "KeepPrivateTags": true, | |
41 "DicomVersion" : "2017c" | |
42 }' > Anonymized.dcm | |
0 | 43 |
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44 **Explanations:** |
0 | 45 |
46 * New UUIDs are automatically generated for the study, the series and | |
47 the instance. | |
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48 * The DICOM tags can be specified either by their name |
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49 (``PatientName``) or by their hexadecimal identifier (in the example |
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50 above, ``0010-1001`` corresponds to ``Other Patient Names``). |
0 | 51 * ``Replace`` is an associative array that associates a DICOM tag with its |
52 new string value. The value is dynamically cast to the proper DICOM | |
53 data type (an HTTP error will occur if the cast fails). Replacements | |
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54 are applied after all the tags to anonymize have been removed. |
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55 You may also use the ``Replace`` field to add new tags to the file. |
0 | 56 * ``Keep`` specifies a list of tags that should be preserved from full |
57 anonymization. | |
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58 * If ``KeepPrivateTags`` is set to ``true`` in the JSON request, |
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59 private tags (i.e. manufacturer-specific tags) are not removed by |
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60 the anonymization process. The default behavior consists in removing |
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61 the private tags, as such tags can contain patient-specific |
0 | 62 information. |
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63 * ``DicomVersion`` specifies which version of the DICOM standard shall |
692 | 64 be used for anonymization. Allowed values are ``2008``, ``2017c``, |
65 or ``2021b`` (new in Orthanc 1.9.4). This parameter has been | |
66 introduced in Orthanc 1.3.0. In earlier version, the ``2008`` | |
67 standard was used. If the parameter is absent, the highest version | |
68 that is supported by Orthanc is used. | |
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69 * ``Remove`` can also be used to provide a list of tags to be manually |
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70 deleted. |
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71 |
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72 **Important:** Starting with Orthanc 1.9.4, the ``Replace``, ``Keep`` |
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73 and ``Remove`` fields can also specify sequences, using the same |
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74 syntax as the ``dcmodify`` command-line tool (wildcards are supported |
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75 as well). Earlier versions were limited to top-level tags in the DICOM |
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76 dataset. Check out the integration test ``test_modify_subsequences`` |
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77 for `examples |
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78 <https://hg.orthanc-server.com/orthanc-tests/file/default/Tests/Tests.py>`__. |
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79 |
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80 **Implementation:** Internally, the setup of the anonymization |
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81 profiles can be found in the methods ``SetupAnonymizationXXX()`` of |
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82 the class ``Orthanc::DicomModification`` (cf. `source code |
763 | 83 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.9.7/OrthancFramework/Sources/DicomParsing/DicomModification.cpp>`__). |
0 | 84 |
85 | |
86 Modification of a Single Instance | |
87 --------------------------------- | |
88 | |
89 Orthanc allows to modify a set of specified tags in a single DICOM | |
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90 instance and to download the resulting modified DICOM file (without |
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91 storing the modified DICOM instance into Orthanc). Example:: |
0 | 92 |
444 | 93 $ curl -X POST http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/modify \ |
94 --data '{ | |
95 "Replace": { | |
96 "PatientName":"hello", | |
97 "PatientID":"world" | |
98 }, | |
99 "Remove":[ | |
100 "InstitutionName" | |
101 ], | |
102 "RemovePrivateTags": true, | |
103 "Force": true, | |
104 "Transcode": "1.2.840.10008.1.2.4.70" | |
105 }' > Modified.dcm | |
0 | 106 |
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107 **Remarks:** |
0 | 108 |
109 * The ``Remove`` array specifies the list of the tags to remove. | |
110 * The ``Replace`` associative array specifies the substitions to be applied (cf. anonymization). | |
112
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111 * If ``RemovePrivateTags`` is set to ``true``, the private tags |
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112 (i.e. manufacturer-specific tags) are removed. |
444 | 113 * The ``Transcode`` option allows you to define the TransferSyntax |
114 of the modified file. | |
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115 * The ``Force`` option must be set to ``true``, in order to allow the |
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116 modification of the ``PatientID``, as such a modification of the |
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117 :ref:`DICOM identifiers <dicom-identifiers>` might lead to breaking |
113 | 118 the DICOM model of the real-world. In general, any explicit |
119 modification to one of the ``PatientID``, ``StudyInstanceUID``, | |
120 ``SeriesInstanceUID``, and ``SOPInstanceUID`` requires ``Force`` to | |
121 be set to ``true``, in order to prevent any unwanted side effect. | |
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122 |
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123 .. highlight:: json |
0 | 124 |
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125 * To replace a sequence of tags, you may use this syntax:: |
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126 |
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127 |
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128 { |
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129 "Replace" : { |
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130 "ProcedureCodeSequence" : [ |
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131 { |
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132 "CodeValue" : "2", |
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133 "CodingSchemeDesignator" : "1", |
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134 "CodeMeaning": "1" |
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135 } |
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136 ] |
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137 } |
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138 } |
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139 |
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140 * To replace a binary tag, you should encode it in base64 and use:: |
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141 |
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142 { |
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143 "Replace" : { |
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144 "EncryptedAttributesSequence" : [ |
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145 { |
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146 "EncryptedContentTransferSyntaxUID" : "1.2.840.10008.1.2", |
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147 "EncryptedContent" : "data:application/octet-stream;base64,SSB3YXMgaGVyZSBpbiAyMDE5LiAgTWFydHkgTWNGbHku" |
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148 } |
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149 ] |
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150 } |
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151 } |
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152 |
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153 |
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154 **Important:** Similarly to anonymization, starting with Orthanc |
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155 1.9.4, the ``Replace``, ``Keep`` and ``Remove`` fields can also |
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156 specify sequences, using the same syntax as the ``dcmodify`` |
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157 command-line tool (wildcards are supported as well). Earlier versions |
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158 were limited to top-level tags in the DICOM dataset. Check out the |
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159 integration test ``test_modify_subsequences`` for `examples |
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160 <https://hg.orthanc-server.com/orthanc-tests/file/default/Tests/Tests.py>`__. |
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161 |
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162 |
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163 .. _study-modification: |
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164 |
0 | 165 Modification of Studies or Series |
166 --------------------------------- | |
167 | |
168 .. highlight:: bash | |
169 | |
170 It is possible to modify all the instances from a study or from a | |
171 series in a single request. In this case, the modified instances are | |
172 stored back into the Orthanc store. Here is how to modify a series:: | |
173 | |
174 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
175 | |
176 | |
177 .. highlight:: json | |
178 | |
179 The parameters are identical to those used to modify a single | |
180 instance. Orthanc will answer a JSON message that tells where the | |
181 modified series has been stored:: | |
182 | |
183 { | |
184 "ID" : "3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce", | |
185 "Path" : "/series/3bd3d343-82879d86-da77321c-1d23fd6b-faa07bce" | |
186 } | |
187 | |
188 | |
189 .. highlight:: bash | |
190 | |
191 Similarly, here is an interaction to modify a study:: | |
192 | |
193 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
194 | |
195 .. highlight:: json | |
196 | |
197 :: | |
198 | |
199 { | |
200 "ID" : "1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28", | |
201 "Path" : "/studies/1c3f7bf4-85b4aa20-236e6315-5d450dcc-3c1bcf28" | |
202 } | |
203 | |
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204 Pay attention to the fact that Orthanc implements safety checks to |
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205 preserve the :ref:`DICOM model of the real world <model-world>`. These |
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206 checks prevent the modification of some tags that are known to belong |
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207 to a level in the patient/study/series/instance hierarchy that is |
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208 higher than the level that corresponds to the REST API call. For |
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209 instance, the tag ``PatientID`` cannot be modified if using the |
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210 ``/studies/{id}/modify`` route (in the latter case, the |
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211 ``/patients/{id}/modify`` route must be used, cf. next section). You |
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212 also have to set the ``Force`` argument to ``true`` if modifying one |
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213 of the :ref:`DICOM identifiers tags <orthanc-ids>` |
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214 (i.e. ``PatientID``, ``StudyInstanceUID``, ``SeriesInstanceUID`` and |
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215 ``SOPInstanceUID``). |
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216 |
0 | 217 |
218 Modification of Patients | |
219 ------------------------ | |
220 | |
221 .. highlight:: bash | |
222 | |
223 Starting with Orthanc 0.7.5, Orthanc can also modify all the instances | |
224 of a patient with a single REST call. Here is a sample:: | |
225 | |
112
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226 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/modify -X POST -d '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}' |
0 | 227 |
228 .. highlight:: json | |
229 | |
230 :: | |
231 | |
232 { | |
233 "ID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
234 "Path" : "/patients/f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
235 "PatientID" : "f7ff9e8b-7bb2e09b-70935a5d-785e0cc5-d9d0abf0", | |
236 "Type" : "Patient" | |
237 } | |
238 | |
239 Please note that, in this case, you have to set the value of the | |
240 ``PatientID (0010,0020)`` tag for Orthanc to accept this modification: | |
241 This is a security to prevent the merging of patient data before and | |
242 after anonymization, if the user does not explicitly tell Orthanc to | |
243 do so. | |
244 | |
245 | |
246 Anonymization of Patients, Studies or Series | |
247 -------------------------------------------- | |
248 | |
249 .. highlight:: bash | |
250 | |
251 Study and series can be anonymized the same way as they are modified:: | |
252 | |
253 $ curl http://localhost:8042/patients/6fb47ef5-072f4557-3215aa29-f99515c1-6fa22bf0/anonymize -X POST -d '{}' | |
254 $ curl http://localhost:8042/studies/ef2ce55f-9342856a-aee23907-2667e859-9f3b734d/anonymize -X POST -d '{}' | |
255 $ curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/anonymize -X POST -d '{}' | |
256 | |
257 As written above, the anonymization process can be fine-tuned by using | |
258 a JSON body. | |
167 | 259 |
260 | |
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261 .. _bulk-modification: |
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262 |
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263 Bulk modification or anonymization |
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264 ---------------------------------- |
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265 |
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266 Starting with Orthanc 1.9.4, it is possible to use the new routes |
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267 ``/tools/bulk-modify`` and ``/tools/bulk-anonymize`` to respectively |
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268 modify or anonymize a set of multiple DICOM resources that are not |
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269 related (i.e. that don't share any parent DICOM resource). A typical |
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270 use case is to modify/anonymize a list of DICOM instances that don't |
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271 belong to the same parent patient/study/series. |
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272 |
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273 .. highlight:: bash |
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274 |
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275 These two routes accept the same arguments as described above, but |
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276 must also be provided with an additional argument ``Resources`` that |
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277 lists the :ref:`Orthanc identifiers <orthanc-ids>` of the resources of |
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278 interest (that may indifferently correspond to patients, studies, |
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279 series or instances). Here are two sample calls:: |
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280 |
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281 $ curl http://localhost:8042/tools/bulk-modify -d '{"Replace":{"SeriesDescription":"HELLO"},"Resources":["b6da0b16-a25ae9e7-1a80fc33-20df01a9-a6f7a1b0","d6634d97-24379e4a-1e68d3af-e6d0451f-e7bcd3d1"]}' |
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282 $ curl http://localhost:8042/tools/bulk-anonymize -d '{"Resources":["b6da0b16-a25ae9e7-1a80fc33-20df01a9-a6f7a1b0","d6634d97-24379e4a-1e68d3af-e6d0451f-e7bcd3d1"]}' |
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283 |
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284 .. highlight:: json |
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285 |
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286 The output of the modification/anonymization lists all the resources |
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287 that have been altered by the call (including their parents). Here is |
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288 the output of the second sample above:: |
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289 |
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290 { |
712 | 291 "Description" : "REST API", |
292 "FailedInstancesCount" : 0, | |
293 "InstancesCount" : 2, | |
294 "IsAnonymization" : true, | |
295 "Resources" : [ | |
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296 { |
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297 "ID" : "04c04806-27b01a5a-08ea66cb-cb36c8b9-ebe62fe3", |
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298 "Path" : "/instances/04c04806-27b01a5a-08ea66cb-cb36c8b9-ebe62fe3", |
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299 "Type" : "Instance" |
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300 }, |
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301 { |
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302 "ID" : "4e37fce9-6b33b8ba-7bb378e1-abc7e2c4-fca4ade3", |
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303 "Path" : "/instances/4e37fce9-6b33b8ba-7bb378e1-abc7e2c4-fca4ade3", |
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304 "Type" : "Instance" |
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305 }, |
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306 { |
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307 "ID" : "6438ee62-b58a4788-517931b3-e10321eb-d1ab2613", |
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308 "Path" : "/series/6438ee62-b58a4788-517931b3-e10321eb-d1ab2613", |
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309 "Type" : "Series" |
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310 }, |
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311 { |
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312 "ID" : "660494fd-1ddd661b-4358d996-ba600e5a-066d94cc", |
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313 "Path" : "/studies/660494fd-1ddd661b-4358d996-ba600e5a-066d94cc", |
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314 "Type" : "Study" |
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315 }, |
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316 { |
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317 "ID" : "5faa0bf8-8a45520b-3a07e536-fc24f241-f59ae3e1", |
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318 "Path" : "/patients/5faa0bf8-8a45520b-3a07e536-fc24f241-f59ae3e1", |
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319 "Type" : "Patient" |
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320 } |
712 | 321 ] |
322 } | |
711
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323 |
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324 |
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325 |
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326 .. _split-merge: |
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327 |
167 | 328 Split/merge of DICOM studies |
329 ---------------------------- | |
330 | |
178 | 331 Starting with Orthanc 1.5.0, Orthanc supports splitting and merging |
167 | 332 DICOM studies through its REST API. |
333 | |
224
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334 .. _split: |
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335 |
167 | 336 Splitting |
337 ^^^^^^^^^ | |
338 | |
339 Here is the syntax to **split** a DICOM study:: | |
340 | |
341 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/split -d \ | |
342 '{"Series":["6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"],"Replace":{"PatientName":"HELLO"},"Remove":["AccessionNumber"]}' | |
343 | |
344 By issuing this command, the series whose :ref:`Orthanc identifier | |
345 <dicom-identifiers>` is | |
346 ``6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228``, and that is part of | |
347 the source study with identifier | |
348 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``, will be removed from | |
349 the source study, and will be moved to a brand new study. | |
350 | |
351 This is done by generating a new value for all the following DICOM | |
352 tags in the DICOM instances of the series of interest: | |
353 ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID (0x0020, | |
354 0x000e)``, and ``SOPInstanceUID (0x0008, 0x0018)``. Here are the | |
355 arguments of this ``/studies/{study}/split`` URI: | |
356 | |
357 * ``Series`` gives the list of series to be separated from the parent | |
358 study (mandatory option). These series must all be children of the | |
359 same source study, that is specified in the URI. | |
360 * ``Replace`` allows to overwrite the DICOM tags that are part of the | |
361 "Patient Module Attributes" and the "General Study Module | |
362 Attributes", as specified by the DICOM 2011 standard in Tables C.7-1 | |
363 and C.7-3. | |
364 * ``Remove`` allows to remove DICOM tags from the same modules as in | |
365 the ``Replace`` options. | |
366 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
367 Orthanc to keep a copy of the original series in the source study. | |
368 By default, the original series are deleted from Orthanc. | |
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369 |
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370 .. _merge: |
167 | 371 |
372 Merging | |
373 ^^^^^^^ | |
374 | |
375 Here is the syntax to **merge** DICOM series, into another DICOM study:: | |
376 | |
377 $ curl http://localhost:8042/studies/6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12/merge -d \ | |
378 '{"Resources":["ef2ce55f-9342856a-aee23907-2667e859-9f3b734d"]}' | |
379 | |
380 By issuing this command, the DICOM series whose :ref:`Orthanc | |
381 identifier <dicom-identifiers>` is | |
382 ``ef2ce55f-9342856a-aee23907-2667e859-9f3b734d``, will be merged into | |
383 target study with identifier | |
384 ``6e2c0ec2-5d99c8ca-c1c21cee-79a09605-68391d12``. | |
385 | |
386 As in the case of splitting, this is done by updating the following | |
387 DICOM tags: ``StudyInstanceUID (0x0020, 0x000d)``, ``SeriesInstanceUID | |
388 (0x0020, 0x000e)``, and ``SOPInstanceUID (0x0008, | |
389 0x0018)``. Furthermore, all the DICOM tags that are part of the | |
390 "Patient Module Attributes" and the "General Study Module Attributes" | |
391 (as specified by the DICOM 2011 standard in Tables C.7-1 and C.7-3), | |
392 are modified to match the target study. Here are the | |
393 arguments of this ``/studies/{study}/merge`` URI: | |
394 | |
395 * ``Resources`` gives the list of source studies or source series | |
396 that are to be merged into the target study. | |
397 * ``KeepSource`` (Boolean value), if set to ``true``, instructs | |
398 Orthanc to keep the source studies and series. By default, the | |
399 original resources are deleted from Orthanc. |