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Aba lvl atlases #114

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Aba lvl atlases #114

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abc9a14
add new multi-level aba atlases
amrka Mar 2, 2026
b8ed015
add new atlases to snakebids
amrka Mar 2, 2026
5f4d8a0
fix the seg files
amrka Mar 2, 2026
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9 changes: 9 additions & 0 deletions spimquant/config/snakebids.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -266,6 +266,15 @@ templates:
roi198:
dseg: 'tpl-ABAv3/tpl-ABAv3_seg-roi198_dseg.nii.gz'
tsv: 'tpl-ABAv3/tpl-ABAv3_seg-roi198_dseg.tsv'
coarse:
dseg: 'tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.nii.gz'
tsv: 'tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.tsv'
mid:
dseg: 'tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.nii.gz'
tsv: 'tpl-ABAv3/tpl-ABAv3_seg-mid_dseg.tsv'
fine:
dseg: 'tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.nii.gz'
tsv: 'tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.tsv'
MouseIn:
# MP2RAGE inv1 chosen since its most similar to the MT GRE I had on hand.. better to create a
# new template later..
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Binary file added spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.nii.gz
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25 changes: 25 additions & 0 deletions spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-coarse_dseg.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
index name abbreviation
1 L_Isocortex L_Isocortex
2 R_Isocortex R_Isocortex
3 L_Olfactory areas L_OLF
4 R_Olfactory areas R_OLF
5 L_Hippocampal formation L_HPF
6 R_Hippocampal formation R_HPF
7 L_Cortical subplate L_CTXsp
8 R_Cortical subplate R_CTXsp
9 L_Striatum L_STR
10 R_Striatum R_STR
11 L_Pallidum L_PAL
12 R_Pallidum R_PAL
13 L_Thalamus L_TH
14 R_Thalamus R_TH
15 L_Hypothalamus L_HY
16 R_Hypothalamus R_HY
17 L_Midbrain L_MB
18 R_Midbrain R_MB
19 L_Pons L_P
20 R_Pons R_P
21 L_Medulla L_MY
22 R_Medulla R_MY
23 L_Cerebellum L_CB
24 R_Cerebellum R_CB
Binary file added spimquant/resources/tpl-ABAv3/tpl-ABAv3_seg-fine_dseg.nii.gz
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