Merge branch 'master' into macatlas

hippunfold/config/snakebids.yml

@@ -128,7 +128,7 @@ parse_args:
   --version:
     help: 'Print the version of HippUnfold'
     action: version
-    version: "1.4.2-pre.41"
+    version: "1.4.2-pre.42"
 
 
   --modality:
@@ -150,9 +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. When using a non-human template, consider using a corresponding atlas. (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. When using a non-human template, consider using a corresponding atlas. (default: %(default)s)'
 
 
 
@@ -162,6 +162,7 @@ parse_args:
       - 'MBMv2'
       - 'MBMv3'
       - 'CIVM'
+      - 'ABAv3'
     default: 'upenn'
     help: 'Set the template to use for shape injection. (default: %(default)s)'
 
@@ -232,6 +233,7 @@ parse_args:
       - 'freesurfer'
       - 'multihist7'
       - 'macaque'
+      - 'mouse'
     default: 
       - 'multihist7'
     nargs: '+'
@@ -385,6 +387,10 @@ template_based_segmentation:
   MBMv3:
     hemi:
       - R
+  ABAv3:
+    hemi:
+      - R
+      - L
 
 
 template_files:
@@ -431,26 +437,42 @@ 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
   macaque:
     label_nii: sub-bigmac_hemi-{hemi}_space-unfold_label-hipp_desc-macaquesubfields_dseg.nii.gz
+    lut: desc-subfields_atlas-macaque_dseg.tsv
     label_list: macaque_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.
@@ -476,7 +498,10 @@ tissue_atlas_mapping:
     dg: 209
     srlm: 227
     cyst: 228
-
+  mouse: 
+    dg: 6
+    srlm: 7
+    cyst: 8
 
 
 rigid_reg_template: False
@@ -510,13 +535,15 @@ resource_urls:
     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='
     macaque: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/6661f504d835c42bcb4cddab/?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/pipeline_description.json

@@ -5,7 +5,7 @@
     "GeneratedBy": [
         {
             "Name": "hippunfold",
-            "Version": "1.4.2-pre.41",
+            "Version": "1.4.2-pre.42",
             "CodeURL": "https://github.com/khanlab/hippunfold",
             "Author": "Jordan DeKraker & Ali Khan",
             "AuthorEmail": "[email protected]"

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()

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hippunfold"
-version = "1.4.2-pre.41"
+version = "1.4.2-pre.42"
 description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)"
 authors = ["Jordan DeKraker & Ali Khan <[email protected]>"]