diff --git a/.dryrun_test_all.sh b/.dryrun_test_all.sh
index f6deb448..d4df830f 100755
--- a/.dryrun_test_all.sh
+++ b/.dryrun_test_all.sh
@@ -1,16 +1,16 @@
 #!/bin/bash
 set -euxo pipefail
 HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w 
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R 
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L 
-hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w 
-hippunfold test_data/bids_T1w test_out participant -np --modality T1w 
-hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
-hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
-hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
-hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
-hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
-hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --use-conda
+# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R 
+# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L 
+# hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w 
+# hippunfold test_data/bids_T1w test_out participant -np --modality T1w 
+# hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
+# hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
+# hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
+# hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
+# hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
+# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
+# hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
+# hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 
diff --git a/hippunfold/workflow/envs/env1.yaml b/hippunfold/workflow/envs/env1.yaml
new file mode 100644
index 00000000..8efea764
--- /dev/null
+++ b/hippunfold/workflow/envs/env1.yaml
@@ -0,0 +1,8 @@
+name: env1
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - nibabel=5.2.1
+  - numpy=2.1.2
\ No newline at end of file
diff --git a/hippunfold/workflow/envs/env2.yaml b/hippunfold/workflow/envs/env2.yaml
new file mode 100644
index 00000000..e21b6f4f
--- /dev/null
+++ b/hippunfold/workflow/envs/env2.yaml
@@ -0,0 +1,7 @@
+name: env2
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - connectome-workbench=2.0.1
\ No newline at end of file
diff --git a/hippunfold/workflow/envs/env3.yaml b/hippunfold/workflow/envs/env3.yaml
new file mode 100644
index 00000000..db9413e4
--- /dev/null
+++ b/hippunfold/workflow/envs/env3.yaml
@@ -0,0 +1,9 @@
+name: env3
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - nibabel=5.2.1
+  - numpy=2.1.2
+  - scipy=1.13.1
\ No newline at end of file
diff --git a/hippunfold/workflow/envs/env4.yaml b/hippunfold/workflow/envs/env4.yaml
new file mode 100644
index 00000000..abe2bcda
--- /dev/null
+++ b/hippunfold/workflow/envs/env4.yaml
@@ -0,0 +1,7 @@
+name: env4
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - ants
\ No newline at end of file
diff --git a/hippunfold/workflow/envs/envAll.yaml b/hippunfold/workflow/envs/envAll.yaml
new file mode 100644
index 00000000..9a6dc006
--- /dev/null
+++ b/hippunfold/workflow/envs/envAll.yaml
@@ -0,0 +1,131 @@
+channels:
+- conda-forge
+- defaults
+dependencies:
+- python=3.9
+- annotated-types=0.7.0
+- appdirs=1.4.4
+- argparse-dataclass=2.0.0
+- arrow=1.3.0
+- astor=0.8.1
+- astroid=2.15.8
+- atomicwrites=1.4.1
+- attrs=23.2.0
+- bids-validator=1.14.6
+- black=22.12.0
+- boutiques=0.5.26
+- certifi=2024.7.4
+- charset-normalizer=3.3.2
+- click=8.1.7
+- colorama=0.4.6
+- conda-inject=1.3.2
+- configargparse=1.7
+- connection-pool=0.0.3
+- copier=9.3.1
+- datrie=0.8.2
+- dill=0.3.8
+- docopt=0.6.2
+- docutils=0.20.1
+- dpath=2.2.0
+- dunamai=1.22.0
+- eval-type-backport=0.2.0
+- fastjsonschema=2.20.0
+- flake8=4.0.1
+- formulaic=0.5.2
+- funcy=2.0
+- gitdb=4.0.11
+- gitpython=3.1.43
+- graphlib-backport=1.1.0
+- greenlet=3.0.3
+- humanfriendly=10.0
+- idna=3.7
+- immutables=0.21
+- importlib-metadata=8.1.0
+- importlib-resources=6.4.0
+- iniconfig=2.0.0
+- interface-meta=1.3.0
+- isort=5.13.2
+- jinja2=3.1.4
+- jinja2-ansible-filters=1.3.2
+- jinja2-time=0.2.0
+- jsonschema=4.23.0
+- jsonschema-specifications=2023.12.1
+- jupyter-core=5.7.2
+- lazy-loader=0.4
+- lazy-object-proxy=1.10.0
+- markupsafe=2.1.5
+- mccabe=0.6.1
+- more-itertools=9.1.0
+- mypy-extensions=1.0.0
+- nbformat=5.10.4
+- nibabel=5.2.1
+- num2words=0.5.13
+- numpy=2.1.2
+- packaging=23.2
+- pandas=2.2.3
+- pastel=0.2.1
+- pathspec=0.12.1
+- pkgutil-resolve-name=1.3.10
+- plac=1.4.3
+- platformdirs=4.2.2
+- pluggy=1.5.0
+- plumbum=1.9.0
+- poethepoet=0.10.0
+- prompt-toolkit=3.0.36
+- psutil=6.0.0
+- pulp=2.7.0
+- pvandyken-deprecated=0.0.4
+- py=1.11.0
+- pybids=0.16.5
+- pycodestyle=2.8.0
+- pydantic=2.9.2
+- pydantic-core=2.23.4
+- pyflakes=2.4.0
+- pygments=2.18.0
+- pygraphviz=1.7
+- pylint=2.17.7
+- pyreadline3=3.4.1
+- pytest=6.2.5
+- pytest-console-scripts=1.4.1
+- python-dateutil=2.9.0.post0
+- pytz=2024.1
+- pywin32=306
+- pyyaml=6.0.1
+- questionary=2.0.1
+- referencing=0.35.1
+- requests=2.32.3
+- reretry=0.11.8
+- rpds-py=0.19.0
+- ruamel-yaml=0.18.6
+- ruamel-yaml-clib=0.2.8
+- scipy=1.13.1
+- simplejson=3.19.2
+- six=1.16.0
+- smart-open=7.0.4
+- smmap=5.0.1
+- snakebids=0.13.1
+- snakefmt=0.8.0
+- snakemake=8.23.0
+- snakemake-interface-common=1.17.4
+- snakemake-interface-executor-plugins=9.3.2
+- snakemake-interface-report-plugins=1.1.0
+- snakemake-interface-storage-plugins=3.3.0
+- sqlalchemy=2.0.31
+- stopit=1.1.2
+- tabulate=0.9.0
+- termcolor=2.4.0
+- throttler=1.2.2
+- toml=0.10.2
+- tomli=2.0.1
+- tomlkit=0.13.0
+- toposort=1.10
+- traitlets=5.14.3
+- types-python-dateutil=2.9.0.20240316
+- typing-extensions=4.12.2
+- tzdata=2024.1
+- urllib3=2.2.2
+- wcwidth=0.2.13
+- wrapt=1.16.0
+- yte=1.5.4
+- zipp=3.19.2
+name: env1
diff --git a/hippunfold/workflow/rules/autotop.smk b/hippunfold/workflow/rules/autotop.smk
index 22e1d4f3..a659faa5 100644
--- a/hippunfold/workflow/rules/autotop.smk
+++ b/hippunfold/workflow/rules/autotop.smk
@@ -66,6 +66,8 @@ rule laplace_coords_hipp:
             hemi="{hemi}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env1.yaml"
     group:
         "subj"
     resources:
@@ -153,6 +155,8 @@ rule prep_equivolume_coords:
             hemi="{hemi}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env1.yaml"
     log:
         bids(
             root="logs",
diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
index 8f26acca..17ef26f3 100644
--- a/hippunfold/workflow/rules/gifti.smk
+++ b/hippunfold/workflow/rules/gifti.smk
@@ -34,6 +34,8 @@ rule cp_template_to_unfold:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -73,6 +75,8 @@ rule calc_unfold_template_coords:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     shadow:
         "minimal"  #this is required to use the temporary files defined as params
     group:
@@ -124,6 +128,8 @@ rule constrain_surf_to_bbox:
             label="{autotop}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env1.yaml"
     log:
         bids(
             root="logs",
@@ -190,6 +196,8 @@ rule warp_gii_unfold2corobl1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -230,6 +238,8 @@ rule correct_bad_vertices1:
             label="hipp",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     container:
@@ -266,6 +276,8 @@ rule calculate_surface_area1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -306,6 +318,8 @@ rule calculate_gyrification1:
             label="hipp",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env2.yaml"
     log:
         bids(
             root="logs",
@@ -354,6 +368,8 @@ rule calculate_curvature_from_surface1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -386,6 +402,8 @@ rule normalize_curvature1:
             label="hipp",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env1.yaml"
     group:
         "subj"
     container:
@@ -432,6 +450,8 @@ rule calculate_thickness_from_surface1:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -486,6 +506,8 @@ rule metric_to_nii:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -568,6 +590,8 @@ rule unfolded_registration:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env4.yaml"
     group:
         "subj"
     log:
@@ -636,6 +660,8 @@ rule warp_gii_unfoldreg:
             label="hipp",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env1.yaml"
     group:
         "subj"
     container:
@@ -743,6 +769,8 @@ rule warp_gii_unfold2corobl2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -781,6 +809,8 @@ rule correct_bad_vertices2:
             label="{autotop}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env3.yaml"
     group:
         "subj"
     container:
@@ -857,6 +887,8 @@ rule affine_gii_to_native:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -889,6 +921,8 @@ rule calculate_surface_area2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -927,6 +961,8 @@ rule calculate_gyrification2:
             label="{autotop}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env2.yaml"
     log:
         bids(
             root="logs",
@@ -972,6 +1008,8 @@ rule calculate_curvature_from_surface2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -1002,6 +1040,8 @@ rule normalize_curvature2:
             label="{autotop}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env1.yaml"
     group:
         "subj"
     container:
@@ -1045,6 +1085,8 @@ rule calculate_thickness_from_surface2:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -1080,6 +1122,8 @@ rule resample_atlas_to_refvol:
             atlas="{atlas}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env4.yaml"
     log:
         bids(
             root="logs",
@@ -1134,6 +1178,8 @@ rule nii_to_label_gii:
             atlas="{atlas}",
             **inputs.subj_wildcards
         ),
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     container:
@@ -1203,6 +1249,8 @@ rule create_dscalar_metric_cifti:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -1269,6 +1317,8 @@ rule create_dlabel_cifti_subfields:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -1478,6 +1528,8 @@ rule create_spec_file_dentate:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
@@ -1512,6 +1564,8 @@ rule merge_lr_spec_file:
         ),
     container:
         config["singularity"]["autotop"]
+    conda:
+        "../envs/env2.yaml"
     group:
         "subj"
     shell:
diff --git a/test_out/.snakebids b/test_out/.snakebids
new file mode 100644
index 00000000..23ff1486
--- /dev/null
+++ b/test_out/.snakebids
@@ -0,0 +1 @@
+{"mode": "bidsapp"}
\ No newline at end of file
diff --git a/test_out/config/snakebids.yml b/test_out/config/snakebids.yml
new file mode 100644
index 00000000..d0417a0f
--- /dev/null
+++ b/test_out/config/snakebids.yml
@@ -0,0 +1,650 @@
+plugins.version.version: 1.5.2rc2
+bids_dir: /local/scratch/hippunfold/test_data/bids_singleT2w
+output_dir: /local/scratch/hippunfold/test_out
+force: true
+debug: false
+derivatives: false
+analysis_levels:
+- participant
+- group
+targets_by_analysis_level:
+  participant: &id001
+  - ''
+  group:
+  - all_group_tsv
+pybids_inputs:
+  T2w:
+    filters:
+      suffix: T2w
+      extension: .nii.gz
+      datatype: anat
+    wildcards:
+    - subject
+    - session
+    - acquisition
+    - run
+  hippb500:
+    filters:
+      suffix: b500
+      extension: .nii.gz
+      invalid_filters: allow
+      datatype: dwi
+    wildcards:
+    - subject
+    - session
+  T1w:
+    filters:
+      suffix: T1w
+      extension: .nii.gz
+      datatype: anat
+    wildcards:
+    - subject
+    - session
+    - acquisition
+    - run
+  manualseg:
+    filters:
+      suffix: dseg
+      extension: .nii.gz
+      datatype: anat
+      invalid_filters: allow
+    wildcards:
+    - subject
+    - session
+    - hemi
+    - acquisition
+    - run
+parse_args:
+  --modality:
+    help: 'Type of image to run hippunfold on. For manualseg and be sure to match
+      the label scheme applied in the look up table (lut) online. For best performance,
+      please also make sure the input is approximately aligned to the template space,
+      with separate hemi-L|R in the name(s). (default: %(default)s)'
+    required: true
+    choices:
+    - T1w
+    - T2w
+    - hippb500
+    - manualseg
+  --template:
+    choices:
+    - CITI168
+    - dHCP
+    - MBMv2
+    - MBMv3
+    - CIVM
+    - ABAv3
+    - bigbrain
+    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, 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)'
+  --inject_template:
+    choices:
+    - upenn
+    - dHCP
+    - MBMv2
+    - MBMv3
+    - CIVM
+    - ABAv3
+    - bigbrain
+    default: upenn
+    help: 'Set the template to use for shape injection. (default: %(default)s)'
+  --use_template_seg:
+    help: 'Use template-based segmentation for hippocampal tissue *instead of* nnUnet
+      and shape injection. This is only to be used if nnUnet models are not trained
+      for the data you are using, e.g. for non-human primate data with the MBMv2 (ex
+      vivo marmoset), MBMv3 (in vivo marmoset), or CIVM (ex vivo macaque) template.
+      (default: %(default)s)'
+    default: false
+    action: store_true
+  --template_seg_smoothing_factor:
+    help: 'Scales the default smoothing sigma for gradient and warp in greedy registration
+      for template-based segmentation. Using a value higher than 1 will use result
+      in a smoother warp. (default: %(default)s)'
+    default: 2.0
+  --skip_preproc:
+    help: 'Set this flag if your inputs (e.g. T2w, dwi) are already pre-processed
+      (default: %(default)s)'
+    default: false
+    action: store_true
+  --skip_coreg:
+    help: 'Set this flag if your inputs (e.g. T2w, dwi) are already registered to
+      T1w space (default: %(default)s)'
+    default: false
+    action: store_true
+  --skip_inject_template_labels:
+    help: 'Set this flag to skip post-processing template injection into CNN segmentation.
+      Note this will disable generation of DG surfaces. (default: %(default)s)'
+    default: false
+    action: store_true
+  --inject_template_smoothing_factor:
+    help: 'Scales the default smoothing sigma for gradient and warp in template shape
+      injection. Using a value higher than 1 will use result in a smoother warp, and
+      greater capacity to patch larger holes in segmentations. Try setting to 2 if
+      nnunet segmentations have large holes. Note: the better solution is to re-train
+      network on the data you are using (default: %(default)s)'
+    default: 1.0
+  --rigid_reg_template:
+    help: 'Use rigid instead of affine for registration to template. Try this if your
+      images are reduced FOV (default: %(default)s)'
+    default: false
+    action: store_true
+  --no_reg_template:
+    help: 'Use if input data is already in space-CITI168 (default: %(default)s)'
+    default: false
+    action: store_true
+  --t1_reg_template:
+    help: 'Use T1w to register to template space, instead of the segmentation modality.
+      Note: this was the default behavior prior to v1.0.0.  (default: %(default)s)'
+    default: false
+    action: store_true
+  --crop_native_res:
+    help: 'Sets the bounding box resolution for the crop native (e.g. cropT1w space).
+      Under the hood, hippUnfold operates at higher resolution than the native image,
+      so this tries to preserve some of that detail. (default: %(default)s)'
+    default: 0.2x0.2x0.2mm
+  --crop_native_box:
+    help: 'Sets the bounding box size for the crop native (e.g. cropT1w space). Make
+      this larger if your hippocampi in crop{T1w,T2w} space are getting cut-off. This
+      must be in voxels (vox) not millimeters (mm). (default: %(default)s)'
+    default: 256x256x256vox
+  --atlas:
+    choices:
+    - bigbrain
+    - magdeburg
+    - freesurfer
+    - multihist7
+    - macaque
+    - mouse
+    default:
+    - multihist7
+    nargs: +
+    help: 'Select the atlas (unfolded space) to use for subfield labels. (default:
+      %(default)s)'
+  --no_unfolded_reg:
+    help: 'Do not perform unfolded space (2D) registration based on thickness, curvature,
+      and gyrification for closer alignment to the reference atlas. NOTE: only multihist7
+      has these features currently, so this unfolded_reg is automatically skipped
+      if a different atlas is chosen. (default: %(default)s)'
+    default: false
+    action: store_true
+  --generate_myelin_map:
+    help: 'Generate myelin map using T1w divided by T2w, and map to surface with ribbon
+      approach. Requires both T1w and T2w images to be present. (default: %(default)s)'
+    default: false
+    action: store_true
+  --use_gpu:
+    help: 'Enable gpu for inference by setting resource gpus=1 in run_inference rule
+      (default: %(default)s)'
+    default: false
+    action: store_true
+  --nnunet_enable_tta:
+    help: 'Enable test-time augmentation for nnU-net inference, slows down inference
+      by 8x, but potentially increases accuracy (default: %(default)s)'
+    default: false
+    action: store_true
+  --output_spaces:
+    choices:
+    - native
+    - T1w
+    nargs: +
+    default:
+    - native
+    help: 'Sets output spaces for results (default: %(default)s)'
+  --output_density:
+    choices:
+    - 0p5mm
+    - 1mm
+    - 2mm
+    - unfoldiso
+    default:
+    - 0p5mm
+    nargs: +
+    help: 'Sets the output vertex density for results. Options correspond to approximate
+      vertex spacings of 0.5mm, 1.0mm, and 2.0mm, respectively, with the unfoldiso
+      (32k hipp) vertices legacy option having unequal vertex spacing. (default: %(default)s)'
+  --hemi:
+    choices:
+    - L
+    - R
+    default:
+    - L
+    - R
+    nargs: +
+    help: 'Hemisphere(s) to process (default: %(default)s)'
+  --laminar_coords_method:
+    choices:
+    - laplace
+    - equivolume
+    default:
+    - equivolume
+    help: 'Method to use for laminar coordinates. Equivolume uses equivolumetric layering
+      from Waehnert et al 2014 (Nighres implementation). (default: %(default)s)'
+  --autotop_labels:
+    choices:
+    - hipp
+    - dentate
+    default:
+    - hipp
+    - dentate
+    nargs: +
+    help: 'Run hipp (CA + subiculum) alone or include dentate (default: %(default)s)'
+  --keep_work:
+    help: 'Keep work folder intact instead of archiving it for each subject (default:
+      %(default)s)'
+    default: false
+    action: store_true
+  --force_nnunet_model:
+    help: 'Force nnunet model to use (expert option). (default: %(default)s)'
+    default: false
+    choices:
+    - T1w
+    - T2w
+    - T1T2w
+    - b1000
+    - trimodal
+    - hippb500
+    - neonateT1w
+    - synthseg_v0.1
+    - synthseg_v0.2
+    - neonateT1w_v2
+  --enable-bids-validation:
+    help: "Enable validation of BIDS dataset. BIDS validation would be performed\n
+      using the bids-validator plugin (if installed/enabled) or with the pybids\n
+      validator implementation (if bids-validator is not installed/enabled).\n"
+    dest: plugins.validator.skip
+    action: store_false
+    default: true
+  --version:
+    help: Print the version of HippUnfold
+    action: version
+    version: 1.5.2-pre.2
+autotop_labels:
+- hipp
+- dentate
+surf_types:
+  hipp:
+  - midthickness
+  - inner
+  - outer
+  dentate:
+  - midthickness
+gifti_metric_types:
+  hipp:
+  - gyrification.shape
+  - curvature.shape
+  - thickness.shape
+  dentate:
+  - gyrification.shape
+  - curvature.shape
+cifti_metric_types:
+  hipp:
+  - gyrification.dscalar
+  - curvature.dscalar
+  - thickness.dscalar
+  dentate:
+  - gyrification.dscalar
+  - curvature.dscalar
+outlier_opts:
+  outlierSmoothDist:
+    unfoldiso: 15
+    0p5mm: 7
+    1mm: 3
+    2mm: 1
+  vertexOutlierThreshold: 3
+singularity:
+  autotop: docker://khanlab/hippunfold_deps:v0.5.1
+xfm_identity: resources/etc/identity_xfm.txt
+xfm_identity_itk: resources/etc/identity_xfm_itk.txt
+template_based_segmentation:
+  CITI168:
+    hemi:
+    - R
+    - L
+  dHCP:
+    hemi:
+    - R
+    - L
+  MBMv2:
+    hemi:
+    - R
+  MBMv3:
+    hemi:
+    - R
+  CIVM:
+    hemi:
+    - R
+    - L
+  upenn:
+    hemi:
+    - R
+  ABAv3:
+    hemi:
+    - R
+    - L
+  bigbrain:
+    hemi:
+    - R
+    - L
+template_files:
+  CITI168:
+    T1w: T1w_head_700um.nii.gz
+    T2w: T2w_head_700um.nii.gz
+    xfm_corobl: CoronalOblique_rigid.txt
+    crop_ref: T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    crop_refT1w: T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    Mask_crop: Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
+    dseg: sub-CITI168_hemi-{hemi}_space-cropT1w_desc-postproc_dseg.nii.gz
+    coords: 
+      sub-CITI168_dir-{dir}_hemi-{hemi}_space-cropT1w_label-{autotop}_desc-laplace_coords.nii.gz
+  dHCP:
+    T1w: tpl-dHCP_cohort-1_res-1_T1w.nii.gz
+    T2w: tpl-dHCP_cohort-1_res-1_T2w.nii.gz
+    xfm_corobl: tpl-dHCP_cohort-1_to-corobl_affine.txt
+    crop_ref: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T2w.nii.gz
+    crop_refT1w: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_T1w.nii.gz
+    Mask_crop: tpl-dHCP_cohort-1_res-1_space-corobl_hemi-{hemi}_desc-hipp_mask.nii.gz
+    dseg: tpl-dHCP_space-corobl_hemi-{hemi}_desc-tissuemanualseg_dseg.nii.gz
+    coords: 
+      tpl-dHCP_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+  MBMv2:
+    T1w: Template_sym_MTR_80um.nii.gz
+    T2w: Template_sym_T2_80um.nii.gz
+    xfm_corobl: tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-MBMv2_hemi-R_space-corobl_{modality}.nii.gz
+    Mask_crop: tpl-MBMv2_hemi-R_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: 
+      tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+  MBMv3:
+    T1w: tpl-MBMv3_T1w.nii.gz
+    T2w: tpl-MBMv3_T2w.nii.gz
+    xfm_corobl: tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-MBMv3_hemi-R_space-corobl_T1w.nii.gz
+    Mask_crop: tpl-MBMv3_hemi-R_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-MBMv3_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: 
+      tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+  CIVM:
+    T1w: tpl-CIVM_T1w.nii.gz
+    xfm_corobl: tpl-CIVM_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-CIVM_hemi-{hemi}_space-corobl_{modality}.nii.gz
+    Mask_crop: tpl-CIVM_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-CIVM_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: 
+      tpl-CIVM_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz
+  upenn:
+    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
+  bigbrain:
+    T1w: tpl-bigbrain_1mm_merker.nii.gz
+    T2w: tpl-bigbrain_1mm_merker.nii.gz
+    xfm_corobl: tpl-bigbrain_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-bigbrain_hemi-{hemi}_space-corobl_100um_merker.nii.gz
+    Mask_crop: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_100um_dseg.nii.gz
+    dseg: tpl-bigbrain_hemi-{hemi}_space-corobl_desc-tissuemanual_100um_dseg.nii.gz
+    coords: 
+      tpl-bigbrain_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-freesurfer_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
+tissue_atlas_mapping:
+  tissue:
+    dg: 8
+    srlm: 2
+    cyst: 7
+  bigbrain:
+    dg: 6
+    srlm: 7
+    cyst: 8
+  multihist7:
+    dg: 6
+    srlm: 7
+    cyst: 8
+  magdeburg:
+    dg: 3
+    srlm: 9
+    cyst: 10
+  freesurfer:
+    dg: 209
+    srlm: 227
+    cyst: 228
+  mouse:
+    dg: 6
+    srlm: 7
+    cyst: 8
+  macaque:
+    dg: 6
+    srlm: 7
+    cyst: 8
+rigid_reg_template: false
+no_reg_template: false
+modality: T2w
+inject_template: upenn
+template: CITI168
+atlas:
+- multihist7
+resource_urls:
+  nnunet_model:
+    T1w: 
+      zenodo.org/record/4508747/files/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar
+    T2w: 
+      zenodo.org/record/4508747/files/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNetTrainerV2.model_best.tar
+    hippb500: 
+      zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar
+    neonateT1w: 
+      zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar
+    neonateT1w_v2: 
+      zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar
+    T1T2w: 
+      zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar
+    synthseg_v0.1: 
+      zenodo.org/record/8184230/files/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar
+    synthseg_v0.2: 
+      zenodo.org/record/8184230/files/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar
+  atlas:
+    multihist7: 
+      files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b782827451220b86dd8/?zip=
+    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=
+    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=
+    bigbrain: 
+      files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/666b1bc765e1de5972893e59/?zip=
+crop_native_box: 256x256x256vox
+crop_native_res: 0.2x0.2x0.2mm
+hippdwi_opts:
+  resample_dim: 734x720x67
+  bbox_x:
+    L: 383 510
+    R: 224 351
+  bbox_y: 198 453
+unfold_vol_ref:
+  hipp:
+    dims:
+    - '256'
+    - '128'
+    - '16'
+    voxdims:
+    - '0.15625'
+    - '0.15625'
+    - '0.15625'
+    origin:
+    - '0'
+    - '200'
+    - '0'
+    extent:
+    - '40'
+    - '20'
+    - '2.5'
+    orient: RPI
+  dentate:
+    dims:
+    - '256'
+    - '32'
+    - '16'
+    voxdims:
+    - '0.15625'
+    - '0.15625'
+    - '0.15625'
+    origin:
+    - '0'
+    - '200'
+    - '0'
+    extent:
+    - '40'
+    - '5'
+    - '2.5'
+    orient: RPI
+unfold_crop_epsilon_fractions:
+- 0
+- 0
+- 1
+unfold_mesh_ref:
+  dims:
+  - 254
+  - 126
+  start:
+  - 0.234375
+  - 0.234375
+  end:
+  - 39.765625
+  - 19.765625
+shape_inject:
+  labels_reg:
+  - 1
+  - 2
+  - 3
+  - 4
+  - 5
+  - 6
+  - 8
+  labels_reinsert:
+  - 7
+  label_smoothing_stdev: 0.5x0.5x0.5mm
+inject_template_smoothing_factor: 1.0
+laplace_labels:
+  AP:
+    gm:
+    - 1
+    - 8
+    src:
+    - 5
+    sink:
+    - 6
+  PD:
+    gm:
+    - 1
+    - 8
+    src:
+    - 3
+    sink:
+    - 8
+  IO:
+    gm:
+    - 1
+    - 8
+    src:
+    - 2
+    - 4
+    - 7
+    sink:
+    - 0
+output_spaces:
+- native
+participant_label:
+exclude_participant_label:
+hemi:
+- L
+- R
+output_density:
+- 0p5mm
+laminar_coords_method:
+- equivolume
+skip_preproc: false
+plugins.validator.skip: true
+nnunet_enable_tta: false
+use_gpu: false
+skip_coreg: false
+keep_work: false
+skip_inject_template_labels: false
+force_nnunet_model: false
+t1_reg_template: false
+generate_myelin_map: false
+no_unfolded_reg: false
+root: .
+use_template_seg: false
+template_seg_smoothing_factor: 2.0
+snakemake_args:
+- -np
+- --use-conda
+pybidsdb_reset: false
+pybidsdb_dir:
+pybids_db_dir:
+pybids_db_reset: <!DEPRECATED!>0<!DEPRECATED!>
+snakemake_target: *id001
+analysis_level: participant
+snakemake_version: 7.32.4
+snakebids_version: 0.13.1
+app_version: 1.5.2rc2
+snakemake_dir: /local/scratch/hippunfold/hippunfold
+snakefile: /local/scratch/hippunfold/hippunfold/workflow/Snakefile