From 74b67aafaa30778997e1c63ce5bddcfd32d93262 Mon Sep 17 00:00:00 2001 From: valosekj Date: Tue, 13 Feb 2024 11:46:05 -0500 Subject: [PATCH 1/5] Add rootlets ground truth labels for 21 images. These 21 images were part of the training dataset D5. For details; see https://github.com/ivadomed/model-spinal-rootlets/tree/main/training --- .../anat/sub-amu01_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-amu05_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-amu05_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-balgrist01_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-balgrist01_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-balgrist02_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-balgrist02_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-balgrist03_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-balgrist03_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-balgrist04_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-balgrist04_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-balgrist06_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-balgrist06_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-barcelona02_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-barcelona02_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-barcelona03_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-barcelona03_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-barcelona06_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-barcelona06_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-brnoUhb01_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-brnoUhb01_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-cardiff02_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-cardiff02_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-cardiff04_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-cardiff04_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-cmrra02_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-cmrra02_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-cmrra04_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-cmrra04_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-geneva01_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-geneva01_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-mgh01_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-mgh01_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-mgh02_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-mgh02_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-stanford02_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-stanford02_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-stanford05_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../sub-stanford05_T2w_label-rootlets_dseg.nii.gz | 1 + .../anat/sub-ucdavis03_T2w_label-rootlets_dseg.json | 11 +++++++++++ .../anat/sub-ucdavis03_T2w_label-rootlets_dseg.nii.gz | 1 + 42 files changed, 252 insertions(+) create mode 100644 derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-balgrist01/anat/sub-balgrist01_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-balgrist01/anat/sub-balgrist01_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-balgrist02/anat/sub-balgrist02_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-balgrist02/anat/sub-balgrist02_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-balgrist03/anat/sub-balgrist03_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-balgrist03/anat/sub-balgrist03_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-barcelona03/anat/sub-barcelona03_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-barcelona03/anat/sub-barcelona03_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-barcelona06/anat/sub-barcelona06_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-barcelona06/anat/sub-barcelona06_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-brnoUhb01/anat/sub-brnoUhb01_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-brnoUhb01/anat/sub-brnoUhb01_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-cardiff02/anat/sub-cardiff02_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-cardiff02/anat/sub-cardiff02_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-cardiff04/anat/sub-cardiff04_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-cardiff04/anat/sub-cardiff04_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-cmrra02/anat/sub-cmrra02_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-cmrra02/anat/sub-cmrra02_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-cmrra04/anat/sub-cmrra04_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-cmrra04/anat/sub-cmrra04_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-geneva01/anat/sub-geneva01_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-geneva01/anat/sub-geneva01_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-mgh01/anat/sub-mgh01_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-mgh01/anat/sub-mgh01_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.nii.gz create mode 100644 derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.json create mode 100644 derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..16fd0a9fca1 --- /dev/null +++ b/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s30820--459e971184aca2428a0033da391340996307e23a423c6a69dda4c6c95328daaf.nii.gz diff --git a/derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": 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a/derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..ad46c88d6df --- /dev/null +++ b/derivatives/labels/sub-balgrist04/anat/sub-balgrist04_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s31457--f6c707cc51182039425389fe55762d5171278c83ac1dfeb0908d22b1af8b9c64.nii.gz diff --git a/derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..4ffdac75911 --- /dev/null +++ b/derivatives/labels/sub-balgrist06/anat/sub-balgrist06_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s30706--6c0364c210d63a076c2af19fa4a3faa4a84832006ce7baaefc7c67b60eea4684.nii.gz diff --git a/derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..c4f56d98ba9 --- /dev/null +++ b/derivatives/labels/sub-barcelona02/anat/sub-barcelona02_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s30916--ab5650ca16ed5a7ec2e41e6643094fda9667883084418843748043b14ea04a23.nii.gz diff --git a/derivatives/labels/sub-barcelona03/anat/sub-barcelona03_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-barcelona03/anat/sub-barcelona03_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-barcelona03/anat/sub-barcelona03_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + 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--git a/derivatives/labels/sub-brnoUhb01/anat/sub-brnoUhb01_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-brnoUhb01/anat/sub-brnoUhb01_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-brnoUhb01/anat/sub-brnoUhb01_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-brnoUhb01/anat/sub-brnoUhb01_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-brnoUhb01/anat/sub-brnoUhb01_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..e4b98734a0d --- /dev/null +++ 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--- /dev/null +++ b/derivatives/labels/sub-mgh01/anat/sub-mgh01_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s31520--b83da9596319659e3d16ee9825e99a89026f30417469969a5d1abb36484a759c.nii.gz diff --git a/derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..6f393313405 --- /dev/null +++ b/derivatives/labels/sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s30604--64d936afcd0502db5a956bdd72d15c165edf886c3b001ec83d0ba12a38925cc0.nii.gz diff --git a/derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..6fb1241db8e --- /dev/null +++ b/derivatives/labels/sub-stanford02/anat/sub-stanford02_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s27378--bd4e7caa6c448e87a34f08a0826e5834c95200f19607f6fd0c64953dc608d34e.nii.gz diff --git a/derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..8e1534eb1e4 --- /dev/null +++ b/derivatives/labels/sub-stanford05/anat/sub-stanford05_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s28037--17ded355895987d8a1e96deb1aa6a359f423b0362fa0da8ef531b5ff0e39a170.nii.gz diff --git a/derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.json b/derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.json new file mode 100644 index 00000000000..5c86ce64e96 --- /dev/null +++ b/derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.json @@ -0,0 +1,11 @@ +{ + "SpatialReference": "orig", + "GeneratedBy": [ + { + "Name": "Manual", + "Author": "Jan Valosek, Theo Mathieu", + "Description": "Manually corrected ground truth labels of dorsal rootlets C2-C8 used to train the model M5; details: https://github.com/ivadomed/model-spinal-rootlets/pull/23#issuecomment-1836305457", + "Date": "2023-12-01" + } + ] +} diff --git a/derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.nii.gz new file mode 100644 index 00000000000..1bf66d105e6 --- /dev/null +++ b/derivatives/labels/sub-ucdavis03/anat/sub-ucdavis03_T2w_label-rootlets_dseg.nii.gz @@ -0,0 +1 @@ +/annex/objects/SHA256E-s31709--2f12768ed73f60f4b263fd97075d2dabfd7b11b6f9265f53399aec05c24a4e9c.nii.gz From 50e011c7bd8a27797401db25c48d776b68ad7329 Mon Sep 17 00:00:00 2001 From: valosekj Date: Tue, 13 Feb 2024 12:23:00 -0500 Subject: [PATCH 2/5] Add rootlets ground truth labels for 3 images. These labels come from 4 manual raters and the STAPLE algorithm and were part of the testing dataset D5. For details; see https://github.com/ivadomed/model-spinal-rootlets/tree/main/training and https://github.com/ivadomed/model-spinal-rootlets/issues/17 --- ...sub-amu02_T2w_label-rootlets_dseg_desc-rater1.json | 11 +++++++++++ ...b-amu02_T2w_label-rootlets_dseg_desc-rater1.nii.gz | 1 + ...sub-amu02_T2w_label-rootlets_dseg_desc-rater2.json | 11 +++++++++++ ...b-amu02_T2w_label-rootlets_dseg_desc-rater2.nii.gz | 1 + ...sub-amu02_T2w_label-rootlets_dseg_desc-rater3.json | 11 +++++++++++ ...b-amu02_T2w_label-rootlets_dseg_desc-rater3.nii.gz | 1 + ...sub-amu02_T2w_label-rootlets_dseg_desc-rater4.json | 11 +++++++++++ ...b-amu02_T2w_label-rootlets_dseg_desc-rater4.nii.gz | 1 + ...sub-amu02_T2w_label-rootlets_dseg_desc-staple.json | 11 +++++++++++ ...b-amu02_T2w_label-rootlets_dseg_desc-staple.nii.gz | 1 + ...rcelona01_T2w_label-rootlets_dseg_desc-rater1.json | 11 +++++++++++ ...elona01_T2w_label-rootlets_dseg_desc-rater1.nii.gz | 1 + ...rcelona01_T2w_label-rootlets_dseg_desc-rater2.json | 11 +++++++++++ ...elona01_T2w_label-rootlets_dseg_desc-rater2.nii.gz | 1 + ...rcelona01_T2w_label-rootlets_dseg_desc-rater3.json | 11 +++++++++++ ...elona01_T2w_label-rootlets_dseg_desc-rater3.nii.gz | 1 + ...rcelona01_T2w_label-rootlets_dseg_desc-rater4.json | 11 +++++++++++ ...elona01_T2w_label-rootlets_dseg_desc-rater4.nii.gz | 1 + ...rcelona01_T2w_label-rootlets_dseg_desc-staple.json | 11 +++++++++++ ...elona01_T2w_label-rootlets_dseg_desc-staple.nii.gz | 1 + ...brnoUhb03_T2w_label-rootlets_dseg_desc-rater1.json | 11 +++++++++++ ...noUhb03_T2w_label-rootlets_dseg_desc-rater1.nii.gz | 1 + ...brnoUhb03_T2w_label-rootlets_dseg_desc-rater2.json | 11 +++++++++++ ...noUhb03_T2w_label-rootlets_dseg_desc-rater2.nii.gz | 1 + ...brnoUhb03_T2w_label-rootlets_dseg_desc-rater3.json | 11 +++++++++++ ...noUhb03_T2w_label-rootlets_dseg_desc-rater3.nii.gz | 1 + ...brnoUhb03_T2w_label-rootlets_dseg_desc-rater4.json | 11 +++++++++++ ...noUhb03_T2w_label-rootlets_dseg_desc-rater4.nii.gz | 1 + ...brnoUhb03_T2w_label-rootlets_dseg_desc-staple.json | 11 +++++++++++ ...noUhb03_T2w_label-rootlets_dseg_desc-staple.nii.gz | 1 + 30 files changed, 180 insertions(+) create mode 100644 derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater1.json create mode 100644 derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater1.nii.gz create mode 100644 derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater2.json create mode 100644 derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater2.nii.gz create mode 100644 derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater3.json create mode 100644 derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater3.nii.gz create mode 100644 derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater4.json create mode 100644 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sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-rater2.json => sub-amu02_T2w_desc-rater2_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-rater2.nii.gz => sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-rater3.json => sub-amu02_T2w_desc-rater3_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-rater3.nii.gz => sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-rater4.json => sub-amu02_T2w_desc-rater4_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-rater4.nii.gz => sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater1.json => sub-barcelona01_T2w_desc-rater1_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater1.nii.gz => sub-barcelona01_T2w_desc-rater1_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater2.json => sub-barcelona01_T2w_desc-rater2_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater2.nii.gz => sub-barcelona01_T2w_desc-rater2_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater3.json => sub-barcelona01_T2w_desc-rater3_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater3.nii.gz => sub-barcelona01_T2w_desc-rater3_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater4.json => sub-barcelona01_T2w_desc-rater4_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-rater4.nii.gz => sub-barcelona01_T2w_desc-rater4_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater1.json => sub-brnoUhb03_T2w_desc-rater1_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater1.nii.gz => sub-brnoUhb03_T2w_desc-rater1_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater2.json => sub-brnoUhb03_T2w_desc-rater2_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater2.nii.gz => sub-brnoUhb03_T2w_desc-rater2_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater3.json => sub-brnoUhb03_T2w_desc-rater3_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater3.nii.gz => sub-brnoUhb03_T2w_desc-rater3_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater4.json => sub-brnoUhb03_T2w_desc-rater4_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater4.nii.gz => sub-brnoUhb03_T2w_desc-rater4_label-rootlets_dseg.nii.gz} (100%) diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater1.json b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater1.json rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater1.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater1.nii.gz rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater2.json b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater2.json rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater2.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater2.nii.gz rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater3.json b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater3.json rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater3.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater3.nii.gz rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater4.json b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater4.json rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater4.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-rater4.nii.gz rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater1.json b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater1_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater1.json rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater1_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater1.nii.gz b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater1_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater1.nii.gz rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater1_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater2.json b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater2_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater2.json rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater2_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater2.nii.gz b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater2_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater2.nii.gz rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater2_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater3.json b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater3_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater3.json rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater3_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater3.nii.gz b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater3_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater3.nii.gz rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater3_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater4.json b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater4_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater4.json rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater4_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater4.nii.gz b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater4_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-rater4.nii.gz rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-rater4_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater1.json b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater1_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater1.json rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater1_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater1.nii.gz b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater1_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater1.nii.gz rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater1_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater2.json b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater2_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater2.json rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater2_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater2.nii.gz b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater2_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater2.nii.gz rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater2_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater3.json b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater3_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater3.json rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater3_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater3.nii.gz b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater3_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater3.nii.gz rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater3_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater4.json b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater4_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater4.json rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater4_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater4.nii.gz b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater4_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-rater4.nii.gz rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-rater4_label-rootlets_dseg.nii.gz From ed1626386cae86b70f75396c6a609f68f5ce7db9 Mon Sep 17 00:00:00 2001 From: valosekj Date: Wed, 3 Apr 2024 12:48:10 -0400 Subject: [PATCH 4/5] Do NOT use 'desc-staple' at the filenames end --- ...le.json => sub-amu02_T2w_desc-staple_label-rootlets_dseg.json} | 0 ...ii.gz => sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz} | 0 ...n => sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.json} | 0 ...=> sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.nii.gz} | 0 ...son => sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.json} | 0 ...z => sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.nii.gz} | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-staple.json => sub-amu02_T2w_desc-staple_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-amu02/anat/{sub-amu02_T2w_label-rootlets_dseg_desc-staple.nii.gz => sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-staple.json => sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-barcelona01/anat/{sub-barcelona01_T2w_label-rootlets_dseg_desc-staple.nii.gz => sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.nii.gz} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-staple.json => sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.json} (100%) rename derivatives/labels/sub-brnoUhb03/anat/{sub-brnoUhb03_T2w_label-rootlets_dseg_desc-staple.nii.gz => sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.nii.gz} (100%) diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-staple.json b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-staple.json rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-staple.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-amu02/anat/sub-amu02_T2w_label-rootlets_dseg_desc-staple.nii.gz rename to derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-staple.json b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-staple.json rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-staple.nii.gz b/derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_label-rootlets_dseg_desc-staple.nii.gz rename to derivatives/labels/sub-barcelona01/anat/sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.nii.gz diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-staple.json b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.json similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-staple.json rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.json diff --git a/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-staple.nii.gz b/derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.nii.gz similarity index 100% rename from derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_label-rootlets_dseg_desc-staple.nii.gz rename to derivatives/labels/sub-brnoUhb03/anat/sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.nii.gz From 3400331fa55208a17a4d34bb9c99ecbc86b93414 Mon Sep 17 00:00:00 2001 From: valosekj Date: Tue, 4 Mar 2025 15:20:47 -0500 Subject: [PATCH 5/5] reorient rootlets labels to RPI --- .../sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz | 2 +- .../sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-balgrist01_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-balgrist02_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-balgrist03_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-balgrist04_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-balgrist06_T2w_label-rootlets_dseg.nii.gz | 2 +- .../sub-barcelona01_T2w_desc-rater1_label-rootlets_dseg.nii.gz | 2 +- .../sub-barcelona01_T2w_desc-rater2_label-rootlets_dseg.nii.gz | 2 +- .../sub-barcelona01_T2w_desc-rater3_label-rootlets_dseg.nii.gz | 2 +- .../sub-barcelona01_T2w_desc-rater4_label-rootlets_dseg.nii.gz | 2 +- .../sub-barcelona01_T2w_desc-staple_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-barcelona02_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-barcelona03_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-barcelona06_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-brnoUhb01_T2w_label-rootlets_dseg.nii.gz | 2 +- .../sub-brnoUhb03_T2w_desc-rater1_label-rootlets_dseg.nii.gz | 2 +- .../sub-brnoUhb03_T2w_desc-rater2_label-rootlets_dseg.nii.gz | 2 +- .../sub-brnoUhb03_T2w_desc-rater3_label-rootlets_dseg.nii.gz | 2 +- .../sub-brnoUhb03_T2w_desc-rater4_label-rootlets_dseg.nii.gz | 2 +- .../sub-brnoUhb03_T2w_desc-staple_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-cardiff02_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-cardiff04_T2w_label-rootlets_dseg.nii.gz | 2 +- .../sub-cmrra02/anat/sub-cmrra02_T2w_label-rootlets_dseg.nii.gz | 2 +- .../sub-cmrra04/anat/sub-cmrra04_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-geneva01_T2w_label-rootlets_dseg.nii.gz | 2 +- .../sub-mgh01/anat/sub-mgh01_T2w_label-rootlets_dseg.nii.gz | 2 +- .../sub-mgh02/anat/sub-mgh02_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-stanford02_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-stanford05_T2w_label-rootlets_dseg.nii.gz | 2 +- .../anat/sub-ucdavis03_T2w_label-rootlets_dseg.nii.gz | 2 +- 36 files changed, 36 insertions(+), 36 deletions(-) diff --git a/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz index 16fd0a9fca1..a9082bb346b 100644 --- a/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz +++ b/derivatives/labels/sub-amu01/anat/sub-amu01_T2w_label-rootlets_dseg.nii.gz @@ -1 +1 @@ -/annex/objects/SHA256E-s30820--459e971184aca2428a0033da391340996307e23a423c6a69dda4c6c95328daaf.nii.gz +/annex/objects/SHA256E-s30905--dd7c35eead8633437e22e322bd218a072c1df6a599c1acb7275fb03c894f8a69.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz index 0562248ff87..f267f0c7f96 100644 --- a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz +++ b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater1_label-rootlets_dseg.nii.gz @@ -1 +1 @@ -/annex/objects/SHA256E-s231587--703bb31bbda6fac63f90a68ca79fef013df708ef2ef13e2ac7545dbee4f08c6b.nii.gz +/annex/objects/SHA256E-s231653--b98667c95501ec8caa15dfd8af6ba341c93ebd6a78afe7de25c5c30cd6ce7e3b.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz index 488146263e6..4adaf2c2f2f 100644 --- a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz +++ b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater2_label-rootlets_dseg.nii.gz @@ -1 +1 @@ -/annex/objects/SHA256E-s52750--01e484b62bc7bc5f3a9927b5eaf9cb57f7855beb814f0f5c740cec50440ac386.nii.gz +/annex/objects/SHA256E-s231689--1b18e0d5c2343d2b62668f0887de38c3d41a03be24cd1bc6d43e12feb6558b8d.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz index fa36a0fe689..b1877ac1dae 100644 --- a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz +++ b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater3_label-rootlets_dseg.nii.gz @@ -1 +1 @@ -/annex/objects/SHA256E-s231033--b8ac5ca846227008a5ed2f576bc37526552da982201a435c261009abb1b5748a.nii.gz +/annex/objects/SHA256E-s231042--0b21759520fb60292eb31838a62454690d0c145b3db0fdb69bed080a90f94734.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz index 89478d55472..4334ac70aa6 100644 --- a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz +++ b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-rater4_label-rootlets_dseg.nii.gz @@ -1 +1 @@ -/annex/objects/SHA256E-s232263--5342e0d69dd0894c9a66334e3b83519a978beee422906b89e31211135727ccbc.nii.gz +/annex/objects/SHA256E-s232254--7556c30d50406d37e8888811117ac6ebe66b886f277b726dcd21437ad19cf4ac.nii.gz diff --git a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz index e1deab9afa1..cd6559125f4 100644 --- a/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz +++ b/derivatives/labels/sub-amu02/anat/sub-amu02_T2w_desc-staple_label-rootlets_dseg.nii.gz @@ -1 +1 @@ -/annex/objects/SHA256E-s7576--04f1f68df8013befa96d9734828889119bfadf472c0aeb9be369789dcb336ef5.nii.gz +/annex/objects/SHA256E-s30359--09054cffdd545b4d10f3bfbeca5c8cbabe2574471246ad83a025b3c88ae8db88.nii.gz diff --git a/derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.nii.gz b/derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.nii.gz index c02c1ddfd36..e8e70542994 100644 --- a/derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.nii.gz +++ b/derivatives/labels/sub-amu05/anat/sub-amu05_T2w_label-rootlets_dseg.nii.gz @@ -1 +1 @@ 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