automated nidm example computation from github action

bids-standard · May 22, 2024 · 35f64a6 · 35f64a6
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diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_con_f_proc.jsonld b/examples/from_parsers/afni/afni_con_f_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_con_f_proc_block.jsonld b/examples/from_parsers/afni/afni_con_f_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_default_proc.jsonld b/examples/from_parsers/afni/afni_default_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_default_proc_block.jsonld b/examples/from_parsers/afni/afni_default_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_gam_proc.jsonld b/examples/from_parsers/afni/afni_gam_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_gam_proc_block.jsonld b/examples/from_parsers/afni/afni_gam_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_other_template_proc.jsonld b/examples/from_parsers/afni/afni_other_template_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_other_template_proc_block.jsonld b/examples/from_parsers/afni/afni_other_template_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
@@ -4,7 +4,7 @@
   "Records": {
     "Software": [
       {
-        "@id": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
+        "@id": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "Label": "AFNI",
@@ -13,115 +13,115 @@
     ],
     "Activities": [
       {
-        "@id": "urn:38c32689-25e4-4616-a55f-99f621b66dae",
+        "@id": "urn:9565c071-19d4-4502-8f50-acf69e458431",
         "Label": "3dpc",
-        "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
+        "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
         "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}",
         "Parameters": {},
         "Used": [
-          "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
-          "urn:854a0da7-0140-4007-b23a-63c8036c2338"
+          "urn:242c05a1-10e3-45a9-aa34-8e4799bf79d6",
+          "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9"
         ]
       },
       {
-        "@id": "urn:40d467e3-1a17-401c-a6fe-fc6b2df21dfd",
+        "@id": "urn:f2905fa3-7c8d-4629-bc94-3108b1af34f2",
         "Label": "3dresample",
-        "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
+        "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
         "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"",
         "Parameters": {},
         "Used": [
-          "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
-          "urn:dee38932-e432-45ac-9034-ec463c0c71d4"
+          "urn:5deae2c5-d728-4f5b-9d1e-3ac865f0e162",
+          "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9"
         ]
       },
       {
-        "@id": "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
+        "@id": "urn:b281ae59-f7ca-40e4-a206-7c9fc41d6a24",
         "Label": "3dMatch",
-        "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
+        "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
         "Command": "3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED",
         "Parameters": {},
         "Used": [
-          "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
-          "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5",
-          "urn:f653dfb6-d7f8-4895-8e06-573f04121f8c"
+          "urn:643c3f61-e81e-440d-9d0a-da03147eb483",
+          "urn:a02c3dfa-efee-4642-a8db-093fed35d380",
+          "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9"
         ]
       },
       {
-        "@id": "urn:f6360992-6c3c-4790-874c-7469907d535a",
+        "@id": "urn:71b7fd66-39e5-4104-bec8-598dafdea9cc",
         "Label": "3dcalc",
-        "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
+        "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
         "Command": "3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
         "Parameters": {},
         "Used": [
-          "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5"
+          "urn:643c3f61-e81e-440d-9d0a-da03147eb483"
         ]
       }
     ],
     "Entities": [
       {
-        "@id": "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
+        "@id": "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:854a0da7-0140-4007-b23a-63c8036c2338",
+        "@id": "urn:242c05a1-10e3-45a9-aa34-8e4799bf79d6",
         "Label": "${grp_dset}",
         "AtLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:270d4b00-919d-46a5-8bd3-ba90ab4de77c",
+        "@id": "urn:ef481cba-a841-48ab-91a2-700b3b045a3e",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}",
-        "GeneratedBy": "urn:38c32689-25e4-4616-a55f-99f621b66dae",
+        "GeneratedBy": "urn:9565c071-19d4-4502-8f50-acf69e458431",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:dee38932-e432-45ac-9034-ec463c0c71d4",
+        "@id": "urn:5deae2c5-d728-4f5b-9d1e-3ac865f0e162",
         "Label": "\"${ref_dset}\"",
         "AtLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:f653dfb6-d7f8-4895-8e06-573f04121f8c",
+        "@id": "urn:a02c3dfa-efee-4642-a8db-093fed35d380",
         "Label": "tmp_REF_DSET.nii.gz",
         "AtLocation": "tmp_REF_DSET.nii.gz",
-        "GeneratedBy": "urn:40d467e3-1a17-401c-a6fe-fc6b2df21dfd",
+        "GeneratedBy": "urn:f2905fa3-7c8d-4629-bc94-3108b1af34f2",
         "digest": {
           "sha256": "e943c60b478a75e89c043bc4a7a6e6c629c3f075007ff501f7b2ab3a253e8d3d"
         }
       },
       {
-        "@id": "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5",
+        "@id": "urn:643c3f61-e81e-440d-9d0a-da03147eb483",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:af09e210-3d42-4ab8-881e-63b8a79ac26f",
+        "@id": "urn:0fc01c72-be31-41da-8050-498c6fc2f72d",
         "Label": "tmp_MATCHED",
         "AtLocation": "tmp_MATCHED",
-        "GeneratedBy": "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
+        "GeneratedBy": "urn:b281ae59-f7ca-40e4-a206-7c9fc41d6a24",
         "digest": {
           "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
         }
       },
       {
-        "@id": "urn:11801d7e-8459-47fd-bfb3-024e9bf5501d",
+        "@id": "urn:e3486423-f966-4ef5-be39-ed9946ed911d",
         "Label": "PC_hyp${num}_sign0.nii.gz",
         "AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
-        "GeneratedBy": "urn:f6360992-6c3c-4790-874c-7469907d535a",
+        "GeneratedBy": "urn:71b7fd66-39e5-4104-bec8-598dafdea9cc",
         "digest": {
           "sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
         }

diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld
@@ -4,7 +4,7 @@
   "Records": {
     "Software": [
       {
-        "@id": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+        "@id": "urn:c9c41032-a75b-4535-84cd-acb432b3d541",
         "RRID": "RRID:SCR_007037",
         "@type": "prov:SoftwareAgent",
         "Label": "AFNI",
@@ -13,93 +13,93 @@
     ],
     "Activities": [
       {
-        "@id": "urn:a0ac5b56-4d0f-4af6-aea6-5c921500a958",
+        "@id": "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
         "Label": "",
-        "AssociatedWith": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+        "AssociatedWith": "urn:c9c41032-a75b-4535-84cd-acb432b3d541",
         "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}; ",
         "Used": [
-          "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
-          "urn:8cb2d405-f78e-461f-a680-56abf991cd9e"
+          "urn:4349b024-08f7-4723-831a-77a19b4c1144",
+          "urn:f40d24fd-8ee7-4822-b98b-3e889411760e"
         ]
       },
       {
-        "@id": "urn:cfaa20a5-21e5-49c6-bfed-2d23065164c6",
+        "@id": "urn:51b6566c-ac9f-4514-a29a-2047f479b665",
         "Label": "block ...",
-        "AssociatedWith": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+        "AssociatedWith": "urn:c9c41032-a75b-4535-84cd-acb432b3d541",
         "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"; 3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED; 3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz; ",
         "Used": [
-          "urn:3629a684-e3d0-4d02-b46c-ba0aa897ca06",
-          "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
-          "urn:1b27e140-7a1e-44d0-b08b-6050245e2a3d",
-          "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
-          "urn:1b27e140-7a1e-44d0-b08b-6050245e2a3d"
+          "urn:05fbe4f8-2e63-4f9b-8d24-0b6839d69dc6",
+          "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
+          "urn:6fb270cb-246a-489a-9655-358899756167",
+          "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
+          "urn:6fb270cb-246a-489a-9655-358899756167"
         ]
       }
     ],
     "Entities": [
       {
-        "@id": "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+        "@id": "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:8cb2d405-f78e-461f-a680-56abf991cd9e",
+        "@id": "urn:4349b024-08f7-4723-831a-77a19b4c1144",
         "Label": "${grp_dset}",
         "AtLocation": "${grp_dset}",
         "digest": {
           "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
         }
       },
       {
-        "@id": "urn:5bcbb31a-da10-4a45-b7eb-04dac91e5b3c",
+        "@id": "urn:d7653c13-bc89-4e81-99a2-e4f6cc895c5b",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}",
-        "GeneratedBy": "urn:a0ac5b56-4d0f-4af6-aea6-5c921500a958",
+        "GeneratedBy": "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
         "digest": {
           "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
         }
       },
       {
-        "@id": "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+        "@id": "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
         "Label": "${dset_mask}",
         "AtLocation": "${dset_mask}",
         "digest": {
           "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
         }
       },
       {
-        "@id": "urn:3629a684-e3d0-4d02-b46c-ba0aa897ca06",
+        "@id": "urn:05fbe4f8-2e63-4f9b-8d24-0b6839d69dc6",
         "Label": "\"${ref_dset}\"",
         "AtLocation": "\"${ref_dset}\"",
         "digest": {
           "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
         }
       },
       {
-        "@id": "urn:1b27e140-7a1e-44d0-b08b-6050245e2a3d",
+        "@id": "urn:6fb270cb-246a-489a-9655-358899756167",
         "Label": "PC_hyp${num}",
         "AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
         "digest": {
           "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
         }
       },
       {
-        "@id": "urn:8c6a8fad-4a10-4e63-902e-cb713291e98b",
+        "@id": "urn:b13a8837-4e83-4ffe-8583-44ad77c778bf",
         "Label": "tmp_MATCHED",
         "AtLocation": "tmp_MATCHED",
-        "GeneratedBy": "urn:cfaa20a5-21e5-49c6-bfed-2d23065164c6",
+        "GeneratedBy": "urn:51b6566c-ac9f-4514-a29a-2047f479b665",
         "digest": {
           "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
         }
       },
       {
-        "@id": "urn:2a27b562-f2c8-4d65-87e7-8324ee4b0b9a",
+        "@id": "urn:d8969622-62e2-4899-b5bc-b94a3a671e93",
         "Label": "PC_hyp${num}_sign0.nii.gz",
         "AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
-        "GeneratedBy": "urn:cfaa20a5-21e5-49c6-bfed-2d23065164c6",
+        "GeneratedBy": "urn:51b6566c-ac9f-4514-a29a-2047f479b665",
         "digest": {
           "sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
         }