From bceaac10ea99dd34dde58df5bbef6bd3b723561d Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Wed, 12 Jun 2024 10:20:24 -0400 Subject: [PATCH] LUTs to OSF for easier additions in the future --- .../desc-subfields_atlas-bigbrain_dseg.tsv | 9 ------ .../desc-subfields_atlas-freesurfer_dseg.tsv | 10 ------- .../desc-subfields_atlas-magdeburg_dseg.tsv | 9 ------ .../desc-subfields_atlas-mouse_dseg.tsv | 9 ------ .../desc-subfields_atlas-multihist7_dseg.tsv | 9 ------ .../label_lut/desc-subfields_dseg.tsv | 9 ------ .../desc-subfields_freeview_desg.tsv | 10 ------- hippunfold/resources/label_lut/dseg.tsv | 29 ------------------- hippunfold/workflow/rules/qc.smk | 6 ++-- 9 files changed, 3 insertions(+), 97 deletions(-) delete mode 100644 hippunfold/resources/label_lut/desc-subfields_atlas-bigbrain_dseg.tsv delete mode 100644 hippunfold/resources/label_lut/desc-subfields_atlas-freesurfer_dseg.tsv delete mode 100644 hippunfold/resources/label_lut/desc-subfields_atlas-magdeburg_dseg.tsv delete mode 100644 hippunfold/resources/label_lut/desc-subfields_atlas-mouse_dseg.tsv delete mode 100644 hippunfold/resources/label_lut/desc-subfields_atlas-multihist7_dseg.tsv delete mode 100644 hippunfold/resources/label_lut/desc-subfields_dseg.tsv delete mode 100644 hippunfold/resources/label_lut/desc-subfields_freeview_desg.tsv delete mode 100644 hippunfold/resources/label_lut/dseg.tsv diff --git a/hippunfold/resources/label_lut/desc-subfields_atlas-bigbrain_dseg.tsv b/hippunfold/resources/label_lut/desc-subfields_atlas-bigbrain_dseg.tsv deleted file mode 100644 index b4293fbe..00000000 --- a/hippunfold/resources/label_lut/desc-subfields_atlas-bigbrain_dseg.tsv +++ /dev/null @@ -1,9 +0,0 @@ -index name abbreviation -1 subiculum Sub -2 CA1 CA1 -3 CA2 CA2 -4 CA3 CA3 -5 CA4 CA4 -6 dentate_gyrus DG -7 SRLM SRLM -8 cysts Cyst diff --git a/hippunfold/resources/label_lut/desc-subfields_atlas-freesurfer_dseg.tsv b/hippunfold/resources/label_lut/desc-subfields_atlas-freesurfer_dseg.tsv deleted file mode 100644 index 95a20f78..00000000 --- a/hippunfold/resources/label_lut/desc-subfields_atlas-freesurfer_dseg.tsv +++ /dev/null @@ -1,10 +0,0 @@ -index name abbreviation -203 parasubiculum ParaSub -204 presubiculum PreSub -205 subiculum Sub -206 CA1 CA1 -208 CA3 CA3 -209 CA4_and_dentate gyrus CA4_DG -226 tail Tail -227 SRLM SRLM -228 cysts Cyst diff --git a/hippunfold/resources/label_lut/desc-subfields_atlas-magdeburg_dseg.tsv b/hippunfold/resources/label_lut/desc-subfields_atlas-magdeburg_dseg.tsv deleted file mode 100644 index 3c0ee0f1..00000000 --- a/hippunfold/resources/label_lut/desc-subfields_atlas-magdeburg_dseg.tsv +++ /dev/null @@ -1,9 +0,0 @@ -index name abbreviation -1 CA1 CA1 -2 CA2 CA2 -3 dentate_gyrus DG -4 CA3 CA3 -5 tail Tail -8 subiculum Sub -9 SRLM SRLM -10 cysts Cyst diff --git a/hippunfold/resources/label_lut/desc-subfields_atlas-mouse_dseg.tsv b/hippunfold/resources/label_lut/desc-subfields_atlas-mouse_dseg.tsv deleted file mode 100644 index b4293fbe..00000000 --- a/hippunfold/resources/label_lut/desc-subfields_atlas-mouse_dseg.tsv +++ /dev/null @@ -1,9 +0,0 @@ -index name abbreviation -1 subiculum Sub -2 CA1 CA1 -3 CA2 CA2 -4 CA3 CA3 -5 CA4 CA4 -6 dentate_gyrus DG -7 SRLM SRLM -8 cysts Cyst diff --git a/hippunfold/resources/label_lut/desc-subfields_atlas-multihist7_dseg.tsv b/hippunfold/resources/label_lut/desc-subfields_atlas-multihist7_dseg.tsv deleted file mode 100644 index b4293fbe..00000000 --- a/hippunfold/resources/label_lut/desc-subfields_atlas-multihist7_dseg.tsv +++ /dev/null @@ -1,9 +0,0 @@ -index name abbreviation -1 subiculum Sub -2 CA1 CA1 -3 CA2 CA2 -4 CA3 CA3 -5 CA4 CA4 -6 dentate_gyrus DG -7 SRLM SRLM -8 cysts Cyst diff --git a/hippunfold/resources/label_lut/desc-subfields_dseg.tsv b/hippunfold/resources/label_lut/desc-subfields_dseg.tsv deleted file mode 100644 index b4293fbe..00000000 --- a/hippunfold/resources/label_lut/desc-subfields_dseg.tsv +++ /dev/null @@ -1,9 +0,0 @@ -index name abbreviation -1 subiculum Sub -2 CA1 CA1 -3 CA2 CA2 -4 CA3 CA3 -5 CA4 CA4 -6 dentate_gyrus DG -7 SRLM SRLM -8 cysts Cyst diff --git a/hippunfold/resources/label_lut/desc-subfields_freeview_desg.tsv b/hippunfold/resources/label_lut/desc-subfields_freeview_desg.tsv deleted file mode 100644 index 899126ce..00000000 --- a/hippunfold/resources/label_lut/desc-subfields_freeview_desg.tsv +++ /dev/null @@ -1,10 +0,0 @@ -#No. Label Name R G B A -1 subiculum 255 0 0 0 -2 CA1 0 255 0 0 -3 CA2 0 0 255 0 -4 CA3 255 255 0 0 -5 CA4 0 255 255 0 -6 dentate_gyrus 255 0 255 0 -7 SRLM 255 239 213 0 -8 cysts 0 0 205 0 - diff --git a/hippunfold/resources/label_lut/dseg.tsv b/hippunfold/resources/label_lut/dseg.tsv deleted file mode 100644 index 7af6d5c0..00000000 --- a/hippunfold/resources/label_lut/dseg.tsv +++ /dev/null @@ -1,29 +0,0 @@ -index name abbreviation -1 right hippocampal grey matter RGM -2 right SRLM or 'dark band' RSRLM -3 right neocortex (entorhinal or parahippocampal) RMTLC -4 right pial surface RPial -5 right hippocampal-amygdalar transition area RHATA -6 right indusium griseum RIndGris -7 right cysts RCyst -8 right dentate gyrus RDG -11 left hippocampal grey matter LGM -12 left SRLM or 'dark band' LSRLM -13 left neocortex (entorhinal or parahippocampal) LMTLC -14 left pial surface LPial -15 left hippocampal-amygdalar transition area LHATA -16 left indusium griseum LIndGris -17 left cysts LCyst -18 left dentate gyrus LDGm -21 right subiculum RSub -22 right CA1 RCA1 -23 right CA2 RCA2 -24 right CA3 RCA3 -25 right CA4 RCA4 -26 right dentate gyrus RDG -31 left subiculum LSub -32 left CA1 LCA1 -33 left CA2 LCA2 -34 left CA3 LCA3 -35 left CA4 LCA4 -36 left dentate gyrus LDG diff --git a/hippunfold/workflow/rules/qc.smk b/hippunfold/workflow/rules/qc.smk index 0e97e6c6..3325110a 100644 --- a/hippunfold/workflow/rules/qc.smk +++ b/hippunfold/workflow/rules/qc.smk @@ -54,9 +54,9 @@ rule get_subfield_vols_subj: hemi=config["hemi"], allow_missing=True, ), - lookup_tsv=Path(workflow.basedir).parent - / "resources" - / "label_lut" + lookup_tsv=Path(download_dir) / + / "atlas" + / "{atlas}" / "desc-subfields_atlas-{atlas}_dseg.tsv", group: "subj"