From 5398c0faf62b02e0475f76498a8af24c0c3722c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sandrine=20B=C3=A9dard?= <71230552+sandrinebedard@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:14:28 -0800 Subject: [PATCH] Rename CSF segmentations in derivatives (#154) * rename CSF segmentations * add code to fix csf orientation and pixdim to correspond with image native space * reorient and resample to native resolution * Revert "reorient and resample to native resolution" This reverts commit f7f3db5827b7cc826588cbe8e78e768914f27303. * Revert "add code to fix csf orientation and pixdim to correspond with image native space" This reverts commit 79e7157a149fe8a73af5d9f18ec3ccfad9ccc901. --------- Co-authored-by: Mathieu Guay-Paquet --- ..._csfseg-manual.json => sub-barcelona05_T2w_label-CSF_seg.json} | 0 ...seg-manual.nii.gz => sub-barcelona05_T2w_label-CSF_seg.nii.gz} | 0 ..._T2w_csfseg-manual.json => sub-cmrrb03_T2w_label-CSF_seg.json} | 0 ..._csfseg-manual.nii.gz => sub-cmrrb03_T2w_label-CSF_seg.nii.gz} | 0 ...T2w_csfseg-manual.json => sub-geneva04_T2w_label-CSF_seg.json} | 0 ...csfseg-manual.nii.gz => sub-geneva04_T2w_label-CSF_seg.nii.gz} | 0 ...2w_csfseg-manual.json => sub-nottwil01_T2w_label-CSF_seg.json} | 0 ...sfseg-manual.nii.gz => sub-nottwil01_T2w_label-CSF_seg.nii.gz} | 0 ...2w_csfseg-manual.json => sub-nottwil03_T2w_label-CSF_seg.json} | 0 ...sfseg-manual.nii.gz => sub-nottwil03_T2w_label-CSF_seg.nii.gz} | 0 ...2w_csfseg-manual.json => sub-nottwil04_T2w_label-CSF_seg.json} | 0 ...sfseg-manual.nii.gz => sub-nottwil04_T2w_label-CSF_seg.nii.gz} | 0 ..._T2w_csfseg-manual.json => sub-pavia04_T2w_label-CSF_seg.json} | 0 ..._csfseg-manual.nii.gz => sub-pavia04_T2w_label-CSF_seg.nii.gz} | 0 ...2w_csfseg-manual.json => sub-perform02_T2w_label-CSF_seg.json} | 0 ...sfseg-manual.nii.gz => sub-perform02_T2w_label-CSF_seg.nii.gz} | 0 ...fseg-manual.json => sub-tokyoIngenia05_T2w_label-CSF_seg.json} | 0 ...-manual.nii.gz => sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz} | 0 ...fseg-manual.json => sub-tokyoIngenia06_T2w_label-CSF_seg.json} | 0 ...-manual.nii.gz => sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz} | 0 20 files changed, 0 insertions(+), 0 deletions(-) rename derivatives/labels/sub-barcelona05/anat/{sub-barcelona05_T2w_csfseg-manual.json => sub-barcelona05_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-barcelona05/anat/{sub-barcelona05_T2w_csfseg-manual.nii.gz => sub-barcelona05_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-cmrrb03/anat/{sub-cmrrb03_T2w_csfseg-manual.json => sub-cmrrb03_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-cmrrb03/anat/{sub-cmrrb03_T2w_csfseg-manual.nii.gz => sub-cmrrb03_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-geneva04/anat/{sub-geneva04_T2w_csfseg-manual.json => sub-geneva04_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-geneva04/anat/{sub-geneva04_T2w_csfseg-manual.nii.gz => sub-geneva04_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-nottwil01/anat/{sub-nottwil01_T2w_csfseg-manual.json => sub-nottwil01_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-nottwil01/anat/{sub-nottwil01_T2w_csfseg-manual.nii.gz => sub-nottwil01_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-nottwil03/anat/{sub-nottwil03_T2w_csfseg-manual.json => sub-nottwil03_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-nottwil03/anat/{sub-nottwil03_T2w_csfseg-manual.nii.gz => sub-nottwil03_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-nottwil04/anat/{sub-nottwil04_T2w_csfseg-manual.json => sub-nottwil04_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-nottwil04/anat/{sub-nottwil04_T2w_csfseg-manual.nii.gz => sub-nottwil04_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-pavia04/anat/{sub-pavia04_T2w_csfseg-manual.json => sub-pavia04_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-pavia04/anat/{sub-pavia04_T2w_csfseg-manual.nii.gz => sub-pavia04_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-perform02/anat/{sub-perform02_T2w_csfseg-manual.json => sub-perform02_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-perform02/anat/{sub-perform02_T2w_csfseg-manual.nii.gz => sub-perform02_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-tokyoIngenia05/anat/{sub-tokyoIngenia05_T2w_csfseg-manual.json => sub-tokyoIngenia05_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-tokyoIngenia05/anat/{sub-tokyoIngenia05_T2w_csfseg-manual.nii.gz => sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz} (100%) rename derivatives/labels/sub-tokyoIngenia06/anat/{sub-tokyoIngenia06_T2w_csfseg-manual.json => sub-tokyoIngenia06_T2w_label-CSF_seg.json} (100%) rename derivatives/labels/sub-tokyoIngenia06/anat/{sub-tokyoIngenia06_T2w_csfseg-manual.nii.gz => sub-tokyoIngenia06_T2w_label-CSF_seg.nii.gz} (100%) diff --git a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.json b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.json rename to derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-barcelona05/anat/sub-barcelona05_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.json b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.json rename to derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-cmrrb03/anat/sub-cmrrb03_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.json b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.json rename to derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-geneva04/anat/sub-geneva04_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.json b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.json rename to derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-nottwil01/anat/sub-nottwil01_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.json b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.json rename to derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-nottwil03/anat/sub-nottwil03_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.json b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.json rename to derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-nottwil04/anat/sub-nottwil04_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.json b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.json rename to derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-pavia04/anat/sub-pavia04_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.json b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.json rename to derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-perform02/anat/sub-perform02_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-perform02/anat/sub-perform02_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.json b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.json similarity index 100% rename from derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.json rename to derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.json diff --git a/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.nii.gz b/derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz similarity index 100% rename from derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_csfseg-manual.nii.gz rename to derivatives/labels/sub-tokyoIngenia05/anat/sub-tokyoIngenia05_T2w_label-CSF_seg.nii.gz diff --git a/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_csfseg-manual.json b/derivatives/labels/sub-tokyoIngenia06/anat/sub-tokyoIngenia06_T2w_label-CSF_seg.json similarity index 100% rename from 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