ABAv3 mouse atlas+template (#299)

* uploaded ABAv3 mouse

* felled missing info

* LUTs to OSF for easier additions in the future

* lint

* snake-friendly formatting

* downloads lists

* lambda for LUT

* atlas_dir as input, filename as param

* updates to use params rather than input

* passing inputs to params

* lint

* typo

* linting back to previous

---------

Co-authored-by: Jordan DeKraker <[email protected]>

hippunfold/config/snakebids.yml

@@ -150,8 +150,9 @@ parse_args:
       - 'MBMv2'
       - 'MBMv3'
       - 'CIVM'
+      - 'ABAv3'
     default: 'CITI168'
-    help: 'Set the template to use for registration to coronal oblique (and optionally for template-based segmentation if --use-template-seg is enabled). CITI168 is for adult human data, dHCP is for neonatal human data, MBMv2 is for ex vivo marmoset data, MBMv3 is for in vivo marmoset data, and CIVM is for in vivo macaque data. (default: %(default)s)'
+    help: 'Set the template to use for registration to coronal oblique (and optionally for template-based segmentation if --use-template-seg is enabled). CITI168 is for adult human data, dHCP is for neonatal human data, MBMv2 is for ex vivo marmoset data, MBMv3 is for in vivo marmoset data, CIVM is for in vivo macaque data, and ABAv3 is for mouse data. (default: %(default)s)'
 
 
 
@@ -162,6 +163,7 @@ parse_args:
       - 'MBMv2'
       - 'MBMv3'
       - 'CIVM'
+      - 'ABAv3'
     default: 'upenn'
     help: 'Set the template to use for shape injection. (default: %(default)s)'
 
@@ -231,6 +233,7 @@ parse_args:
       - 'magdeburg'
       - 'freesurfer'
       - 'multihist7'
+      - 'mouse'
     default: 
       - 'multihist7'
     nargs: '+'
@@ -384,6 +387,10 @@ template_based_segmentation:
   MBMv3:
     hemi:
       - R
+  ABAv3:
+    hemi:
+      - R
+      - L
 
 
 template_files:
@@ -430,23 +437,38 @@ template_files:
     T1w: tpl-upenn_desc-hipptissue_dseg.nii.gz
     dseg: tpl-upenn_desc-hipptissue_dseg.nii.gz
     coords: tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+  ABAv3:
+    T1w: tpl-ABAv3_T1w.nii.gz
+    xfm_corobl: tpl-ABAv3_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-ABAv3_hemi-{hemi}_space-corobl_T1w.nii.gz
+    Mask_crop: tpl-ABAv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
+    dseg: tpl-ABAv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: tpl-ABAv3_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
 
 atlas_files:
   multihist7:
     label_nii: sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
+    lut: desc-subfields_atlas-multihist7_dseg.tsv
     label_list: labellist.txt
     thickness: thickness.nii.gz
     curvature: curvature.nii.gz
     gyrification: gyrification.nii.gz
   bigbrain:
     label_nii: sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
+    lut: desc-subfields_atlas-bigbrain_dseg.tsv
     label_list: sub-bigbrain_labellist.txt
   magdeburg:
     label_nii: sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
+    lut: desc-subfields_atlas-magdeburg_dseg.tsv
     label_list: magdeburg_labellist.txt
   freesurfer:
     label_nii: sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
+    lut: desc-subfields_atlas-mfreesurfer_dseg.tsv
     label_list: freesurfer_labellist.txt
+  mouse:
+    label_nii: sub-ABAv3_space-unfold_label-hipp_desc-mousesubfields_dseg.nii.gz
+    lut: desc-subfields_atlas-mouse_dseg.tsv
+    label_list: mouse_labellist.txt
 
 
 #values to use for re-mapping tissue labels when combining with subfields.
@@ -472,7 +494,10 @@ tissue_atlas_mapping:
     dg: 209
     srlm: 227
     cyst: 228
-
+  mouse: 
+    dg: 6
+    srlm: 7
+    cyst: 8
 
 
 rigid_reg_template: False
@@ -505,13 +530,15 @@ resource_urls:
     bigbrain: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8b13d27b123094c96f/?zip='
     magdeburg: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8013d27b122f94c938/?zip='
     freesurfer: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8513d27b123094c96a/?zip='
+    mouse: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/666884380f8c80103a3c9569/?zip='
   template:
     CITI168: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf0282745121fb86a93/?zip='
     dHCP: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bff13d27b123094c9b4/?zip='
     MBMv2: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0887852d133ca597dd/?zip='
     MBMv3: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0e8a28b11240ffc6e9/?zip='
     upenn: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c1613d27b122a94ca09/?zip='
     CIVM: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf62827451220b86e24/?zip='
+    ABAv3: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/6668855b6b6c8e2cc704ca97/?zip='
 #to get hash, see https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
 
 

hippunfold/workflow/rules/qc.smk

@@ -54,10 +54,10 @@ rule get_subfield_vols_subj:
             hemi=config["hemi"],
             allow_missing=True,
         ),
-        lookup_tsv=Path(workflow.basedir).parent
-        / "resources"
-        / "label_lut"
-        / "desc-subfields_atlas-{atlas}_dseg.tsv",
+        atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
+    params:
+        lookup_tsv=lambda wildcards, input: Path(input.atlas_dir)
+        / config["atlas_files"][wildcards.atlas]["lut"].format(**wildcards),
     group:
         "subj"
     output:

hippunfold/workflow/scripts/gen_volume_tsv.py

@@ -2,7 +2,7 @@
 import pandas as pd
 import numpy as np
 
-lookup_df = pd.read_table(snakemake.input.lookup_tsv, index_col="index")
+lookup_df = pd.read_table(snakemake.params.lookup_tsv, index_col="index")
 
 # get indices and names from lookup table
 indices = lookup_df.index.to_list()