diff --git a/.dryrun_test_all.sh b/.dryrun_test_all.sh index 4dccdf95..bb0e5642 100755 --- a/.dryrun_test_all.sh +++ b/.dryrun_test_all.sh @@ -1,17 +1,17 @@ #!/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_segT2w test_out participant -np --modality segT2w -hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz -hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --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 +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_segT2w test_out participant -np --modality segT2w +hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz +hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --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/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml index 3ae96c8e..7a51a32e 100644 --- a/.github/workflows/python-testing.yml +++ b/.github/workflows/python-testing.yml @@ -35,7 +35,7 @@ jobs: needs: ["quality"] strategy: matrix: - python-version: ["3.7", "3.8", "3.9"] + python-version: ["3.8", "3.9"] steps: - name: Install non-python dependencies diff --git a/.gitignore b/.gitignore index d40c0cdf..68bc17f9 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,160 @@ -hippunfold.egg-info -hippunfold/.snakemake -hippunfold/__pycache__ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ diff --git a/Dockerfile b/Dockerfile index 03364c6d..4916a778 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM khanlab/autotop_deps:v0.4.4-fix +FROM khanlab/hippunfold_deps:v0.5.1 MAINTAINER alik@robarts.ca diff --git a/docs/contributing/contributing.md b/docs/contributing/contributing.md index 79030ef0..f9e92fec 100644 --- a/docs/contributing/contributing.md +++ b/docs/contributing/contributing.md @@ -75,6 +75,10 @@ from the `hippunfold` folder that contains the cd hippunfold snakemake -np +## Wet-run testing your workflow: + +Opensource data has been made available for wet-run testing any changes to HippUnfold on OSF [here](https://osf.io/k2nme/). These are real opensource data meant ot span a wide array of HippUnfold use cases with various modalities, resolutions, developmental stages, and species. Please note that some changes to hippUnfold will impact all worflows and should be run and then visually inspected for all these cases. Other changes may impact only one workflow (e.g. adding a new template) and so the recommended run parameters should be adjusted accordingly. + ## Instructions for Compute Canada This section provides an example of how to set up a `pip installed` copy diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 4a449f0b..4649c022 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -10,6 +10,7 @@ debug: False derivatives: False #will search in bids/derivatives if True; can also be path(s) to derivatives datasets + #list of analysis levels in the bids app analysis_levels: &analysis_levels - participant @@ -35,8 +36,8 @@ pybids_inputs: suffix: 'T2w' extension: '.nii.gz' datatype: 'anat' - invalid_filters: 'allow' - space: null + # invalid_filters: 'allow' + # space: null wildcards: - subject - session @@ -58,8 +59,8 @@ pybids_inputs: suffix: 'T1w' extension: '.nii.gz' datatype: 'anat' - invalid_filters: 'allow' - space: null + # invalid_filters: 'allow' + # space: null wildcards: - subject - session @@ -75,6 +76,8 @@ pybids_inputs: wildcards: - subject - session + - acquisition + - run cropseg: filters: @@ -86,6 +89,9 @@ pybids_inputs: - subject - session - hemi + - acquisition + - run + @@ -93,44 +99,6 @@ pybids_inputs: # passed on the argparse add_argument() parse_args: -#--- core BIDS-app options --- (do not modify below) - - bids_dir: - help: The directory with the input dataset formatted according - to the BIDS standard. - - output_dir: - help: The directory where the output files - should be stored. If you are running group level analysis - this folder should be prepopulated with the results of the - participant level analysis. - - analysis_level: - help: Level of the analysis that will be performed. - choices: *analysis_levels - - --participant_label: - help: The label(s) of the participant(s) that should be analyzed. The label - corresponds to sub- from the BIDS spec - (so it does not include "sub-"). If this parameter is not - provided all subjects should be analyzed. Multiple - participants can be specified with a space separated list. - nargs: '+' - - --exclude_participant_label: - help: The label(s) of the participant(s) that should be excluded. The label - corresponds to sub- from the BIDS spec - (so it does not include "sub-"). If this parameter is not - provided all subjects should be analyzed. Multiple - participants can be specified with a space separated list. - nargs: '+' - - --version: - help: 'Print the version of HippUnfold' - action: version - version: "1.4.2-pre.42" - - --modality: help: 'Type of image to run hippunfold on. Modality prefixed with seg will import an existing (manual) hippocampal tissue segmentation from that space, instead of running neural network (default: %(default)s)' required: True @@ -160,6 +128,7 @@ parse_args: --inject_template: choices: - 'upenn' + - 'dHCP' - 'MBMv2' - 'MBMv3' - 'CIVM' @@ -177,17 +146,11 @@ parse_args: 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 - - --derivatives: - help: 'Path to the derivatives folder (e.g. for finding manual segs) (default: %(default)s) ' - default: False - --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 @@ -330,6 +293,21 @@ parse_args: - neonateT1w_v2 + --enable-bids-validation: + help: | + Enable validation of BIDS dataset. BIDS validation would be performed + using the bids-validator plugin (if installed/enabled) or with the pybids + validator implementation (if bids-validator is not installed/enabled). + dest: "plugins.validator.skip" + action: "store_false" + default: True + + + --version: + help: 'Print the version of HippUnfold' + action: version + version: "1.5.2-pre.2" + # --- surface specific configuration -- @@ -391,16 +369,24 @@ template_based_segmentation: hemi: - R - L - CIVM: + dHCP: hemi: - R - L + MBMv2: hemi: - R MBMv3: hemi: - R + CIVM: + hemi: + - R + - L + upenn: + hemi: + - R ABAv3: hemi: - R @@ -428,22 +414,24 @@ template_files: 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-{hemi}_space-corobl_{modality}.nii.gz - Mask_crop: tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz + 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-{hemi}_space-corobl_T1w.nii.gz - Mask_crop: tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz - dseg: tpl-MBMv3_hemi-{hemi}_space-corobl_desc-tissuemanual_dseg.nii.gz - coords: tpl-MBMv3_dir-{dir}_hemi-{hemi}_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz + 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 @@ -471,6 +459,7 @@ template_files: 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 @@ -489,7 +478,7 @@ atlas_files: 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 + 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 @@ -528,7 +517,10 @@ tissue_atlas_mapping: dg: 6 srlm: 7 cyst: 8 - + macaque: + dg: 6 + srlm: 7 + cyst: 8 rigid_reg_template: False no_reg_template: False @@ -630,6 +622,7 @@ unfold_crop_epsilon_fractions: - 0 - 1 #in unfolded space voxels + # space for uniform unfolded grid: # currently only used for interpolating hipp subfields on surface unfold_mesh_ref: @@ -700,6 +693,7 @@ output_density: laminar_coords_method: equivolume skip_preproc: False +plugins.validator.skip: False nnunet_enable_tta: False use_gpu: False skip_coreg: False diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index 4ff5f350..706e9b97 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -1,14 +1,14 @@ { - "Name": "Snakemake BIDS app for hippocampal unfolding & subfield segmentation", - "BIDSVersion": "1.4.0", - "DatasetType": "derivative", - "GeneratedBy": [ - { - "Name": "hippunfold", - "Version": "1.4.2-pre.42", - "CodeURL": "https://github.com/khanlab/hippunfold", - "Author": "Jordan DeKraker & Ali Khan", - "AuthorEmail": "ali.khan@uwo.ca" + "Name": "Snakemake BIDS app for hippocampal unfolding & subfield segmentation", + "BIDSVersion": "1.8.0", + "DatasetType": "derivative", + "GeneratedBy": [ + { + "Name": "hippunfold", + "Version": "1.5.2-pre.2", + "CodeURL": "https://github.com/khanlab/hippunfold", + "Author": "Jordan DeKraker & Ali Khan", + "AuthorEmail": "ali.khan@uwo.ca" } ] } diff --git a/hippunfold/run.py b/hippunfold/run.py index 0565f7aa..e03b7be5 100755 --- a/hippunfold/run.py +++ b/hippunfold/run.py @@ -1,24 +1,27 @@ #!/usr/bin/env python3 -import os +from pathlib import Path -from snakebids.app import SnakeBidsApp -from snakebids.cli import add_dynamic_args +from snakebids import bidsapp, plugins +if "__file__" not in globals(): + __file__ = "../hippunfold/run.py" -def get_parser(): - """Exposes parser for sphinx doc generation, cwd is the docs dir""" - app = SnakeBidsApp("../hippunfold") - add_dynamic_args(app.parser, app.config["parse_args"], app.config["pybids_inputs"]) - return app.parser + +app = bidsapp.app( + [ + plugins.SnakemakeBidsApp(Path(__file__).resolve().parent), + plugins.BidsValidator(), + plugins.Version(distribution="hippunfold"), + plugins.CliConfig("parse_args"), + plugins.ComponentEdit("pybids_inputs"), + ] +) -def main(): - app = SnakeBidsApp( - os.path.abspath(os.path.dirname(__file__)), - configfile_path="config/snakebids.yml", - ) - app.run_snakemake() +def get_parser(): + """Exposes parser for sphinx doc generation, cwd is the docs dir.""" + return app.build_parser().parser if __name__ == "__main__": - main() + app.run() diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile index 76894097..46b4a248 100644 --- a/hippunfold/workflow/Snakefile +++ b/hippunfold/workflow/Snakefile @@ -1,12 +1,14 @@ # ---- snakebids boilerplate import snakebids -from snakebids import bids +from snakebids import bids, set_bids_spec configfile: "config/snakebids.yml" +set_bids_spec("v0_0_0") + # consider moving this logic to another smk file to clean-up limit_to_list = set() @@ -74,17 +76,13 @@ else: if not config["atlas"] == ["multihist7"]: config["no_unfolded_reg"] = True -# writes inputs_config.yml and updates config dict -config.update( - snakebids.generate_inputs( - bids_dir=config["bids_dir"], - pybids_inputs=config["pybids_inputs"], - derivatives=config["derivatives"], - participant_label=config["participant_label"], - exclude_participant_label=config["exclude_participant_label"], - limit_to=list(limit_to_list), - use_bids_inputs=False, - ) +inputs = snakebids.generate_inputs( + bids_dir=config["bids_dir"], + pybids_inputs=config["pybids_inputs"], + derivatives=config["derivatives"], + participant_label=config["participant_label"], + exclude_participant_label=config["exclude_participant_label"], + limit_to=list(limit_to_list), ) @@ -106,13 +104,17 @@ wildcard_constraints: template="[a-zA-Z0-9]+", -root = os.path.join(config["root"], "hippunfold") -work = os.path.join(config["root"], "work") +root = os.path.normpath(os.path.join(config["root"], "hippunfold")) +work = os.path.normpath(os.path.join(config["root"], "work")) include: "rules/common.smk" include: "rules/download.smk" -include: "rules/preproc_t1.smk" + + +if "T1w" in limit_to_list: + + include: "rules/preproc_t1.smk" # include rules only as they are needed.. diff --git a/hippunfold/workflow/rules/autotop.smk b/hippunfold/workflow/rules/autotop.smk index e267fd82..22e1d4f3 100644 --- a/hippunfold/workflow/rules/autotop.smk +++ b/hippunfold/workflow/rules/autotop.smk @@ -16,7 +16,7 @@ def get_labels_for_laplace(wildcards): seg = bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="postproc", space="corobl", @@ -33,7 +33,7 @@ def get_inputs_laplace(wildcards): bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="hipp", suffix="coords.nii.gz", @@ -64,7 +64,7 @@ rule laplace_coords_hipp: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -73,7 +73,7 @@ rule laplace_coords_hipp: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", hemi="{hemi}", suffix="laplace-hipp.txt" @@ -89,7 +89,7 @@ rule laplace_coords_dentate: coords=bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="dentate", suffix="coords.nii.gz", @@ -107,7 +107,7 @@ rule laplace_coords_dentate: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -116,7 +116,7 @@ rule laplace_coords_dentate: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", hemi="{hemi}", suffix="laplace-dentate.txt" @@ -141,7 +141,7 @@ rule prep_equivolume_coords: suffix="mask.nii.gz", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), innerbin=bids( root=work, @@ -151,12 +151,12 @@ rule prep_equivolume_coords: suffix="mask.nii.gz", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", hemi="{hemi}", suffix="binarize.txt" @@ -179,7 +179,7 @@ rule equivolume_coords: suffix="mask.nii.gz", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), innerbin=bids( root=work, @@ -189,7 +189,7 @@ rule equivolume_coords: suffix="mask.nii.gz", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), params: script=os.path.join(workflow.basedir, "scripts/equivolume_coords.py"), @@ -203,7 +203,7 @@ rule equivolume_coords: desc="equivol", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -212,7 +212,7 @@ rule equivolume_coords: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", hemi="{hemi}", suffix="equivolume.txt" diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk index 4c568f95..9bce0bd6 100644 --- a/hippunfold/workflow/rules/common.smk +++ b/hippunfold/workflow/rules/common.smk @@ -1,3 +1,28 @@ +from appdirs import AppDirs +from snakebids.paths import bids_factory, specs + +from functools import partial + + +def get_single_bids_input(wildcards, component): + """Generic input function for getting the first instance of a bids component + from a dataset, and throw an error if more than one are found. + + Use this in a rule by using e.g.: + in_img = partial(get_single_bids_input,component='T1w') + """ + + subj_inputs = inputs[component].filter(**wildcards).expand() + if len(subj_inputs) > 1: + raise ValueError( + f"Expected 1 input for '{component}' {wildcards}, " + f"but found {len(subj_inputs)}: {subj_inputs}." + f"You can use the --filter-{component} option to filter your wildcards." + ) + else: + return subj_inputs[0] + + # take mean of all scans if >1, otherwise just copy the one scan def get_avg_or_cp_scans_cmd(wildcards, input, output): if len(input) > 1: @@ -24,30 +49,8 @@ def get_modality_suffix(modality): def get_final_spec(): - specs = expand( - bids( - root=root, - datatype="surf", - den="{density}", - space="{space}", - hemi="{hemi}", - label="{autotop}", - suffix="surfaces.spec", - **config["subj_wildcards"], - ), - density=config["output_density"], - space=ref_spaces, - hemi=config["hemi"], - autotop=config["autotop_labels"], - allow_missing=True, - ) - return specs - - -def get_final_surf(): - gii = [] - gii.extend( - expand( + if len(config["hemi"]) == 2: + specs = inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="surf", @@ -56,7 +59,8 @@ def get_final_surf(): space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"], + suffix="surfaces.spec", + **inputs.subj_wildcards, ), density=config["output_density"], space=ref_spaces, @@ -65,9 +69,8 @@ def get_final_surf(): surfname=config["surf_types"]["hipp"], allow_missing=True, ) - ) - gii.extend( - expand( + else: + specs = inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="surf", @@ -76,7 +79,8 @@ def get_final_surf(): space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"], + suffix="surfaces.spec", + **inputs.subj_wildcards, ), density=config["output_density"], space=ref_spaces, @@ -86,11 +90,11 @@ def get_final_surf(): allow_missing=True, ) ) - return gii + return specs def get_final_subfields(): - return expand( + return inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="anat", @@ -99,7 +103,7 @@ def get_final_subfields(): space="{space}", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), hemi=config["hemi"], space=crop_ref_spaces, @@ -117,7 +121,7 @@ def get_final_coords(): coords = [] # compute all laplace coords by default (incl IO) coords.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="coords", @@ -127,7 +131,7 @@ def get_final_coords(): space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), desc="laplace", dir=["AP", "PD", "IO"], @@ -138,7 +142,7 @@ def get_final_coords(): ) ) coords.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="coords", @@ -148,7 +152,7 @@ def get_final_coords(): space="{space}", hemi="{hemi}", label="hipp", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), desc=[desc_io], dir=["IO"], @@ -164,11 +168,11 @@ def get_final_transforms(): xfms = [] xfms.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="xfm.nii.gz", hemi="{hemi}", @@ -184,11 +188,11 @@ def get_final_transforms(): ) xfms.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="xfm.nii.gz", hemi="{hemi}", @@ -204,11 +208,11 @@ def get_final_transforms(): ) xfms.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="refvol.nii.gz", space="unfold", @@ -226,7 +230,7 @@ def get_final_anat(): if "T1w" in ref_spaces or "T2w" in ref_spaces: anat.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="anat", @@ -236,7 +240,7 @@ def get_final_anat(): ), space="{space}", hemi="{hemi}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), space=crop_ref_spaces, hemi=config["hemi"], @@ -251,21 +255,21 @@ def get_final_qc(): if not template_modality == False: qc.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="qc", suffix="regqc.png", from_="{native_modality}", to=config["template"], - **config["subj_wildcards"], + **inputs.subj_wildcards, ), native_modality=template_modality, allow_missing=True, ) ) qc.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="qc", @@ -274,7 +278,7 @@ def get_final_qc(): space="{space}", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), hemi=config["hemi"], atlas=config["atlas"], @@ -283,7 +287,7 @@ def get_final_qc(): ) ) qc.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="qc", @@ -293,7 +297,7 @@ def get_final_qc(): space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), hemi=config["hemi"], autotop=config["autotop_labels"], @@ -304,7 +308,7 @@ def get_final_qc(): ) if len(config["hemi"]) == 2: qc.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="qc", @@ -312,7 +316,7 @@ def get_final_qc(): space="{space}", atlas="{atlas}", suffix="volumes.png", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), space=crop_ref_spaces, atlas=config["atlas"], @@ -322,14 +326,14 @@ def get_final_qc(): if (config["modality"] == "T1w") or (config["modality"] == "T2w"): if not config["use_template_seg"]: qc.extend( - expand( + inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="qc", desc="unetf3d", suffix="dice.tsv", hemi="{hemi}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ), hemi=config["hemi"], allow_missing=True, @@ -362,9 +366,16 @@ def get_final_output(): modality_key = get_modality_key(config["modality"]) # use a zip list for subject/session: - zip_list = config["input_zip_lists"][modality_key] + zip_list = inputs[modality_key].zip_lists if "session" in zip_list: - zip_list = snakebids.filter_list(zip_list, {"session": config["sessions"]}) + zip_list = snakebids.filter_list( + zip_list, + { + "session": inputs[get_modality_key(config["modality"])].zip_lists[ + "session" + ] + }, + ) final_output.extend( expand( @@ -410,17 +421,14 @@ if "corobl" in ref_spaces: def get_final_work_tar(): - return bids( - root=work, - suffix="work.tar.gz", - include_subject_dir=False, - include_session_dir=False, - **config["subj_wildcards"] - ) + bids = bids_factory(specs.v0_0_0(subject_dir=False, session_dir=False)) + return bids(root=work, suffix="work.tar.gz", **inputs.subj_wildcards) def get_work_dir(wildcards): - folder_with_file = expand(bids(root=work, **config["subj_wildcards"]), **wildcards) + folder_with_file = inputs[get_modality_key(config["modality"])].expand( + bids(root=work, **inputs.subj_wildcards), **wildcards + ) folder_without_file = os.path.dirname(folder_with_file[0]) return folder_without_file diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk index 4c317fac..4174253c 100644 --- a/hippunfold/workflow/rules/gifti.smk +++ b/hippunfold/workflow/rules/gifti.smk @@ -30,7 +30,7 @@ rule cp_template_to_unfold: space="unfold", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -69,7 +69,7 @@ rule calc_unfold_template_coords: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -101,7 +101,7 @@ rule constrain_surf_to_bbox: space="unfold", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), ref_nii=bids( root=root, @@ -109,7 +109,7 @@ rule constrain_surf_to_bbox: space="unfold", label="{autotop}", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -122,7 +122,7 @@ rule constrain_surf_to_bbox: unfoldreg="none", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), log: bids( @@ -132,7 +132,7 @@ rule constrain_surf_to_bbox: desc="constrainbbox", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -151,7 +151,7 @@ rule warp_gii_unfold2corobl1: warp=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="hipp", suffix="xfm.nii.gz", hemi="{hemi}", @@ -169,7 +169,7 @@ rule warp_gii_unfold2corobl1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), params: structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi], @@ -186,7 +186,7 @@ rule warp_gii_unfold2corobl1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -211,7 +211,7 @@ rule correct_bad_vertices1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), params: dist=lambda wildcards: config["outlier_opts"]["outlierSmoothDist"][ @@ -228,7 +228,7 @@ rule correct_bad_vertices1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -250,7 +250,7 @@ rule calculate_surface_area1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -262,7 +262,7 @@ rule calculate_surface_area1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -285,7 +285,7 @@ rule calculate_gyrification1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), unfold_surfarea=os.path.join( workflow.basedir, @@ -304,7 +304,7 @@ rule calculate_gyrification1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), log: bids( @@ -315,7 +315,7 @@ rule calculate_gyrification1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -337,7 +337,7 @@ rule calculate_curvature_from_surface1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -350,7 +350,7 @@ rule calculate_curvature_from_surface1: hemi="{hemi}", desc="unnorm", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -372,7 +372,7 @@ rule normalize_curvature1: hemi="{hemi}", desc="unnorm", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -384,7 +384,7 @@ rule normalize_curvature1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -405,7 +405,7 @@ rule calculate_thickness_from_surface1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), outer=bids( root=work, @@ -416,7 +416,7 @@ rule calculate_thickness_from_surface1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -428,7 +428,7 @@ rule calculate_thickness_from_surface1: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -453,7 +453,7 @@ rule metric_to_nii: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), unfoldedsurf=bids( root=work, @@ -465,7 +465,7 @@ rule metric_to_nii: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), atlas_dir=Path(download_dir) / "atlas" / "multihist7", params: @@ -482,7 +482,7 @@ rule metric_to_nii: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -505,7 +505,7 @@ rule unfolded_registration: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), curvature=bids( root=work, @@ -516,7 +516,7 @@ rule unfolded_registration: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), gyrification=bids( root=work, @@ -527,7 +527,7 @@ rule unfolded_registration: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas, params: @@ -544,7 +544,7 @@ rule unfolded_registration: output: warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN", @@ -556,7 +556,7 @@ rule unfolded_registration: ), invwarp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN", @@ -579,7 +579,7 @@ rule unfolded_registration: unfoldreg="{atlas}", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), shadow: "minimal" @@ -599,7 +599,7 @@ rule warp_gii_unfoldreg: invwarp=expand( bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN", @@ -622,7 +622,7 @@ rule warp_gii_unfoldreg: unfoldreg="none", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -634,7 +634,7 @@ rule warp_gii_unfoldreg: space="unfold", hemi="{hemi}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -656,7 +656,7 @@ rule dentate_skip_unfoldreg: unfoldreg="none", hemi="{hemi}", label="dentate", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -668,7 +668,7 @@ rule dentate_skip_unfoldreg: space="unfold", hemi="{hemi}", label="dentate", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -693,7 +693,7 @@ def skip_unfoldreg_option(wildcards): unfoldreg="none", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ) else: gii = bids( @@ -705,7 +705,7 @@ def skip_unfoldreg_option(wildcards): space="unfold", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ) return gii @@ -716,7 +716,7 @@ rule warp_gii_unfold2corobl2: warp=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="xfm.nii.gz", hemi="{hemi}", @@ -739,7 +739,7 @@ rule warp_gii_unfold2corobl2: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -763,7 +763,7 @@ rule correct_bad_vertices2: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), params: dist=lambda wildcards: config["outlier_opts"]["outlierSmoothDist"][ @@ -779,7 +779,7 @@ rule correct_bad_vertices2: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -800,7 +800,7 @@ rule cp_corobl_root: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -811,7 +811,7 @@ rule cp_corobl_root: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -832,12 +832,12 @@ rule affine_gii_to_native: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -853,7 +853,7 @@ rule affine_gii_to_native: space="{native_modality}", hemi="{hemi}", label="{autotop,hipp|dentate}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -874,7 +874,7 @@ rule calculate_surface_area2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -885,7 +885,7 @@ rule calculate_surface_area2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -907,7 +907,7 @@ rule calculate_gyrification2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), unfold_surfarea=os.path.join( workflow.basedir, @@ -925,7 +925,7 @@ rule calculate_gyrification2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), log: bids( @@ -935,7 +935,7 @@ rule calculate_gyrification2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -956,7 +956,7 @@ rule calculate_curvature_from_surface2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -968,7 +968,7 @@ rule calculate_curvature_from_surface2: hemi="{hemi}", desc="unnorm", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -988,8 +988,8 @@ rule normalize_curvature2: space="{space}", hemi="{hemi}", desc="unnorm", - label="hipp", - **config["subj_wildcards"] + label="{autotop}", + **inputs.subj_wildcards ), output: gii=bids( @@ -1000,7 +1000,7 @@ rule normalize_curvature2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -1020,7 +1020,7 @@ rule calculate_thickness_from_surface2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), outer=bids( root=root, @@ -1030,7 +1030,7 @@ rule calculate_thickness_from_surface2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: gii=bids( @@ -1041,7 +1041,7 @@ rule calculate_thickness_from_surface2: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -1063,7 +1063,7 @@ rule resample_atlas_to_refvol: label="hipp", datatype="warps", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas, params: @@ -1078,7 +1078,7 @@ rule resample_atlas_to_refvol: hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), log: bids( @@ -1088,7 +1088,7 @@ rule resample_atlas_to_refvol: hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -1108,7 +1108,7 @@ rule nii_to_label_gii: hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), surf=os.path.join( workflow.basedir, @@ -1132,7 +1132,7 @@ rule nii_to_label_gii: hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -1167,7 +1167,7 @@ def get_inputs_cifti_metric(wildcards): space="{space}", hemi="L", label="{autotop}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ).format(**wildcards), ) if "R" in config["hemi"]: @@ -1180,7 +1180,7 @@ def get_inputs_cifti_metric(wildcards): space="{space}", hemi="R", label="{autotop}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ).format(**wildcards), ) return files @@ -1199,7 +1199,7 @@ rule create_dscalar_metric_cifti: suffix="{metric}.dscalar.nii", space="{space}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -1222,7 +1222,7 @@ def get_inputs_cifti_label(wildcards): space="{space}", hemi="L", label="hipp", - **config["subj_wildcards"], + **inputs.subj_wildcards, ).format(**wildcards), ) if "R" in config["hemi"]: @@ -1236,7 +1236,7 @@ def get_inputs_cifti_label(wildcards): space="{space}", hemi="R", label="hipp", - **config["subj_wildcards"], + **inputs.subj_wildcards, ).format(**wildcards), ) return files @@ -1265,7 +1265,7 @@ rule create_dlabel_cifti_subfields: suffix="subfields.dlabel.nii", space="{space}", label="hipp", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -1315,7 +1315,7 @@ rule cp_unfolded_noconstrain: space="unfold", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -1336,12 +1336,14 @@ rule create_spec_file_hipp: space="{space}", hemi="{hemi}", label="{label}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), metric=get_gifti_metric_types(wildcards.label), allow_missing=True, ), - subfields=lambda wildcards: expand( + subfields=lambda wildcards: inputs[ + get_modality_key(config["modality"]) + ].expand( bids( root=root, datatype="surf", @@ -1351,7 +1353,7 @@ rule create_spec_file_hipp: hemi="{hemi}", label="{label}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), atlas=config["atlas"], allow_missing=True, @@ -1365,13 +1367,15 @@ rule create_spec_file_hipp: space="{space}", hemi="{hemi}", label="{label}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), surfname=["midthickness"], space=["{space}", "unfold"], allow_missing=True, ), - cifti_metrics=lambda wildcards: expand( + cifti_metrics=lambda wildcards: inputs[ + get_modality_key(config["modality"]) + ].expand( bids( root=root, datatype="surf", @@ -1379,12 +1383,14 @@ rule create_spec_file_hipp: suffix="{cifti}.nii", space="{space}", label="{label}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), cifti=get_cifti_metric_types(wildcards.label), allow_missing=True, ), - cifti_labels=lambda wildcards: expand( + cifti_labels=lambda wildcards: inputs[ + get_modality_key(config["modality"]) + ].expand( bids( root=root, datatype="surf", @@ -1393,7 +1399,7 @@ rule create_spec_file_hipp: atlas="{atlas}", space="{space}", label="{label}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), atlas=config["atlas"], allow_missing=True, @@ -1409,7 +1415,7 @@ rule create_spec_file_hipp: hemi="{hemi,L|R}", space="{space}", label="{label,hipp}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -1430,7 +1436,7 @@ rule create_spec_file_dentate: space="{space}", hemi="{hemi}", label="{label}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), metric=get_gifti_metric_types(wildcards.label), allow_missing=True, @@ -1444,7 +1450,7 @@ rule create_spec_file_dentate: space="{space}", hemi="{hemi}", label="{label}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), surfname=["midthickness"], space=["{space}", "unfold"], @@ -1458,7 +1464,7 @@ rule create_spec_file_dentate: suffix="{cifti}.nii", space="{space}", label="{label}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), cifti=get_cifti_metric_types(wildcards.label), allow_missing=True, @@ -1474,7 +1480,7 @@ rule create_spec_file_dentate: hemi="{hemi,L|R}", space="{space}", label="{label,dentate}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -1495,7 +1501,7 @@ rule merge_lr_spec_file: hemi="{hemi}", space="{space}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), hemi=["L", "R"], allow_missing=True, @@ -1508,7 +1514,7 @@ rule merge_lr_spec_file: space="{space}", suffix="surfaces.spec", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] diff --git a/hippunfold/workflow/rules/myelin_map.smk b/hippunfold/workflow/rules/myelin_map.smk index 057e3ffb..573580fd 100644 --- a/hippunfold/workflow/rules/myelin_map.smk +++ b/hippunfold/workflow/rules/myelin_map.smk @@ -8,7 +8,7 @@ rule divide_t1_by_t2: space="corobl", desc="preproc", suffix="T1w.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), t2=bids( root=work, @@ -17,7 +17,7 @@ rule divide_t1_by_t2: space="corobl", desc="preproc", suffix="T2w.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: t1overt2=bids( @@ -27,7 +27,7 @@ rule divide_t1_by_t2: space="corobl", desc="preproc", suffix="T1wDividedByT2w.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -48,7 +48,7 @@ rule create_ribbon: space="{space}", desc="laplace", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: ribbon=bids( @@ -59,7 +59,7 @@ rule create_ribbon: space="{space}", desc="ribbon", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -80,7 +80,7 @@ rule sample_myelin_map_surf: hemi="{hemi}", desc="preproc", suffix="T1wDividedByT2w.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), mid=bids( root=root, @@ -90,7 +90,7 @@ rule sample_myelin_map_surf: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), inner=bids( root=root, @@ -100,7 +100,7 @@ rule sample_myelin_map_surf: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), outer=bids( root=root, @@ -110,7 +110,7 @@ rule sample_myelin_map_surf: space="corobl", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), ribbon=bids( root=work, @@ -120,7 +120,7 @@ rule sample_myelin_map_surf: space="corobl", desc="ribbon", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: metric=bids( @@ -131,7 +131,7 @@ rule sample_myelin_map_surf: space="{space}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk index b9f20b69..04f31515 100644 --- a/hippunfold/workflow/rules/nnunet.smk +++ b/hippunfold/workflow/rules/nnunet.smk @@ -1,44 +1,45 @@ import re -from appdirs import AppDirs def get_nnunet_input(wildcards): - if config["modality"] == "T2w": - nii = ( - bids( - root=work, - datatype="anat", - **config["subj_wildcards"], - suffix="T2w.nii.gz", - space="corobl", - desc="preproc", - hemi="{hemi}", - ), - ) + T1w_nii = bids( + root=work, + datatype="anat", + space="corobl", + desc="preproc", + hemi="{hemi}", + suffix="T1w.nii.gz", + **inputs.subj_wildcards, + ) + T2w_nii = bids( + root=work, + datatype="anat", + space="corobl", + desc="preproc", + hemi="{hemi}", + suffix="T2w.nii.gz", + **inputs.subj_wildcards, + ) + if (config["modality"] == "T1w" or config["modality"] == "T2w") and config[ + "force_nnunet_model" + ] == "T1T2w": + return (T1w_nii, T2w_nii) + + elif config["modality"] == "T2w": + return T2w_nii elif config["modality"] == "T1w": - nii = ( - bids( - root=work, - datatype="anat", - **config["subj_wildcards"], - suffix="T1w.nii.gz", - space="corobl", - desc="preproc", - hemi="{hemi}", - ), - ) + return T1w_nii elif config["modality"] == "hippb500": - nii = bids( + return bids( root=work, datatype="dwi", hemi="{hemi}", space="corobl", suffix="b500.nii.gz", - **config["subj_wildcards"], + **inputs.subj_wildcards, ) else: raise ValueError("modality not supported for nnunet!") - return nii def get_model_tar(): @@ -95,6 +96,19 @@ def parse_trainer_from_tar(wildcards, input): return trainer +def get_cmd_copy_inputs(wildcards, input): + in_img = input.in_img + if isinstance(in_img, str): + # we have one input image + return f"cp {in_img} tempimg/temp_0000.nii.gz" + else: + cmd = [] + # we have multiple input images + for i, img in enumerate(input.in_img): + cmd.append(f"cp {img} tempimg/temp_{i:04d}.nii.gz") + return " && ".join(cmd) + + rule run_inference: """ This rule uses either GPU or CPU . It also runs in an isolated folder (shadow), with symlinks to inputs in that folder, copying over outputs once complete, so temp files are not retained""" @@ -102,7 +116,7 @@ rule run_inference: in_img=get_nnunet_input, model_tar=get_model_tar(), params: - temp_img="tempimg/temp_0000.nii.gz", + cmd_copy_inputs=get_cmd_copy_inputs, temp_lbl="templbl/temp.nii.gz", model_dir="tempmodel", in_folder="tempimg", @@ -115,7 +129,7 @@ rule run_inference: nnunet_seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="nnunet", space="corobl", @@ -124,7 +138,7 @@ rule run_inference: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="nnunet.txt", space="corobl", hemi="{hemi,Lflip|R}" @@ -149,7 +163,7 @@ rule run_inference: # run inference #copy from temp output folder to final output "mkdir -p {params.model_dir} {params.in_folder} {params.out_folder} && " - "cp {input.in_img} {params.temp_img} && " + "{params.cmd_copy_inputs} && " "tar -xf {input.model_tar} -C {params.model_dir} && " "export RESULTS_FOLDER={params.model_dir} && " "export nnUNet_n_proc_DA={threads} && " @@ -163,7 +177,7 @@ rule unflip_nnunet_nii: nnunet_seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="nnunet", space="corobl", @@ -173,7 +187,7 @@ rule unflip_nnunet_nii: bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="{modality}.nii.gz".format(modality=config["modality"]), space="corobl", desc="preproc", @@ -184,7 +198,7 @@ rule unflip_nnunet_nii: nnunet_seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="nnunet", space="corobl", @@ -219,7 +233,7 @@ rule qc_nnunet_f3d: bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="{modality}.nii.gz".format(modality=config["modality"]), space="corobl", desc="preproc", @@ -229,7 +243,7 @@ rule qc_nnunet_f3d: seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="nnunet", space="corobl", @@ -242,7 +256,7 @@ rule qc_nnunet_f3d: cpp=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="cpp.nii.gz", desc="f3d", space="corobl", @@ -251,7 +265,7 @@ rule qc_nnunet_f3d: res=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="{modality}.nii.gz".format(modality=config["modality"]), desc="f3d", space="template", @@ -260,7 +274,7 @@ rule qc_nnunet_f3d: res_mask=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="mask.nii.gz", desc="f3d", space="template", @@ -271,7 +285,7 @@ rule qc_nnunet_f3d: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="qcreg.txt", desc="f3d", space="corobl", @@ -289,7 +303,7 @@ rule qc_nnunet_dice: res_mask=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="mask.nii.gz", desc="f3d", space="template", @@ -312,7 +326,7 @@ rule qc_nnunet_dice: suffix="dice.tsv", desc="unetf3d", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), caption="../report/nnunet_qc.rst", category="Segmentation QC", diff --git a/hippunfold/workflow/rules/preproc_cropseg.smk b/hippunfold/workflow/rules/preproc_cropseg.smk index 7e73dd28..aface7f0 100644 --- a/hippunfold/workflow/rules/preproc_cropseg.smk +++ b/hippunfold/workflow/rules/preproc_cropseg.smk @@ -1,11 +1,12 @@ + rule import_cropseg: input: - config["input_path"]["cropseg"], + in_img=partial(get_single_bids_input, component="cropseg"), output: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", hemi="{hemi,L|R}" @@ -23,7 +24,7 @@ rule lr_flip_seg: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", hemi="{hemi}" @@ -32,7 +33,7 @@ rule lr_flip_seg: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", hemi="{hemi,L}flip" diff --git a/hippunfold/workflow/rules/preproc_hippb500.smk b/hippunfold/workflow/rules/preproc_hippb500.smk index 2bdacb2a..1f07a2ee 100644 --- a/hippunfold/workflow/rules/preproc_hippb500.smk +++ b/hippunfold/workflow/rules/preproc_hippb500.smk @@ -7,7 +7,7 @@ rule resample_hippdwi_to_template: bounding boxes, and keep all Z slices (since is Z is smaller than in template). """ input: - b500=config["input_path"]["hippb500"], + b500=inputs["hippb500"].path, params: resample_dim=config["hippdwi_opts"]["resample_dim"], bbox_x=lambda wildcards: config["hippdwi_opts"]["bbox_x"][wildcards.hemi], @@ -19,7 +19,7 @@ rule resample_hippdwi_to_template: hemi="{hemi,L|R}", space="corobl", suffix="b500.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -40,7 +40,7 @@ rule lr_flip_b500: nii=bids( root=work, datatype="dwi", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="b500.nii.gz", space="corobl", hemi="{hemi}" @@ -49,7 +49,7 @@ rule lr_flip_b500: nii=bids( root=work, datatype="dwi", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="b500.nii.gz", space="corobl", hemi="{hemi,L}flip" @@ -67,7 +67,7 @@ rule cp_b500_to_anat_dir: nii=bids( root=work, datatype="dwi", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="b500.nii.gz", space="corobl", hemi="{hemi}" @@ -80,7 +80,7 @@ rule cp_b500_to_anat_dir: suffix="hippb500.nii.gz", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" diff --git a/hippunfold/workflow/rules/preproc_seg.smk b/hippunfold/workflow/rules/preproc_seg.smk index 1bfbcf86..fbb221cb 100644 --- a/hippunfold/workflow/rules/preproc_seg.smk +++ b/hippunfold/workflow/rules/preproc_seg.smk @@ -1,17 +1,8 @@ rule import_seg: input: - lambda wildcards: expand( - config["input_path"]["seg"], - zip, - **snakebids.filter_list(config["input_zip_lists"]["seg"], wildcards) - )[0], + in_img=partial(get_single_bids_input, component="seg"), output: - bids( - root=work, - datatype="anat", - **config["input_wildcards"]["seg"], - suffix="dseg.nii.gz" - ), + bids(root=work, datatype="anat", **inputs.subj_wildcards, suffix="dseg.nii.gz"), group: "subj" container: @@ -24,15 +15,12 @@ rule import_seg: rule warp_seg_to_corobl_crop: input: nii=bids( - root=work, - datatype="anat", - **config["input_wildcards"]["seg"], - suffix="dseg.nii.gz" + root=work, datatype="anat", **inputs.subj_wildcards, suffix="dseg.nii.gz" ), xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{space}", to="corobl", @@ -47,7 +35,7 @@ rule warp_seg_to_corobl_crop: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", hemi="{hemi,L|R}", @@ -67,7 +55,7 @@ rule lr_flip_seg: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", hemi="{hemi}", @@ -77,7 +65,7 @@ rule lr_flip_seg: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", hemi="{hemi,L}flip", diff --git a/hippunfold/workflow/rules/preproc_t1.smk b/hippunfold/workflow/rules/preproc_t1.smk index 038b0dfb..334f7fe8 100644 --- a/hippunfold/workflow/rules/preproc_t1.smk +++ b/hippunfold/workflow/rules/preproc_t1.smk @@ -2,18 +2,11 @@ ruleorder: compose_template_xfm_corobl > convert_template_xfm_ras2itk rule import_t1: - """Note: this rule only grabs the first T1w - TODO: add motion-corrected averaging, like we do for T2w""" + """TODO: add motion-corrected averaging, like we do for T2w""" input: - lambda wildcards: expand( - config["input_path"]["T1w"], - zip, - **snakebids.filter_list(config["input_zip_lists"]["T1w"], wildcards) - )[0], + in_img=partial(get_single_bids_input, component="T1w"), output: - bids( - root=work, datatype="anat", **config["subj_wildcards"], suffix="T1w.nii.gz" - ), + bids(root=work, datatype="anat", **inputs.subj_wildcards, suffix="T1w.nii.gz"), group: "subj" shell: @@ -24,16 +17,12 @@ if config["skip_preproc"]: rule import_preproc_t1: input: - lambda wildcards: expand( - config["input_path"]["T1w"], - zip, - **snakebids.filter_list(config["input_zip_lists"]["T1w"], wildcards) - )[0], + in_img=partial(get_single_bids_input, component="T1w"), output: bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T1w.nii.gz", desc="preproc" ), @@ -49,14 +38,14 @@ else: t1=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T1w.nii.gz" ), output: t1=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="preproc", suffix="T1w.nii.gz" ), @@ -70,218 +59,20 @@ else: "N4BiasFieldCorrection -d 3 -i {input.t1} -o {output}" -def reg_to_template_cmd(wildcards, input, output): - ref = str( - Path(input.template_dir) - / config["template_files"][config["template"]][wildcards.modality].format( - **wildcards - ), - ) - if config["no_reg_template"]: - cmd = f"reg_resample -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {input.xfm_identity}; cp {input.xfm_identity} {output.xfm_ras}" - elif config["rigid_reg_template"]: - cmd = f"reg_aladin -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {output.xfm_ras} -rigOnly" - else: - cmd = f"reg_aladin -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {output.xfm_ras}" - return cmd - - -rule reg_to_template: - """ generic for T1w or T2w right now """ - input: - flo=bids( - root=root, - datatype="anat", - **config["subj_wildcards"], - desc="preproc", - suffix="{modality}.nii.gz" - ), - xfm_identity=os.path.join(workflow.basedir, "..", config["xfm_identity"]), - template_dir=Path(download_dir) / "template" / config["template"], - params: - cmd=reg_to_template_cmd, - output: - warped_subj=bids( - root=work, - datatype="anat", - **config["subj_wildcards"], - suffix="{modality,T1w|T2w}.nii.gz", - space=config["template"], - desc="affine" - ), - xfm_ras=bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="{modality,T1w|T2w}", - to=config["template"], - desc="affine", - type_="ras" - ), - log: - bids( - root="logs", - **config["subj_wildcards"], - suffix="reg.txt", - from_="{modality,T1w|T2w}", - to=config["template"], - desc="affine", - type_="ras" - ), - container: - config["singularity"]["autotop"] - group: - "subj" - shell: - "{params.cmd}" - - -rule convert_template_xfm_ras2itk: - input: - bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="{reg_suffix}", - to=config["template"], - desc="affine", - type_="ras" - ), - output: - bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="{reg_suffix}", - to=config["template"], - desc="affine", - type_="itk" - ), - container: - config["singularity"]["autotop"] - group: - "subj" - shell: - "c3d_affine_tool {input} -oitk {output}" - - -# now have subject -> template transform, can compose that with template -> corobl to get subject -> corobl -rule compose_template_xfm_corobl: - input: - sub_to_std=bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="T1w", - to=config["template"], - desc="affine", - type_="itk" - ), - template_dir=Path(download_dir) / "template" / config["template"], - params: - std_to_cor=lambda wildcards, input: Path(input.template_dir) - / config["template_files"][config["template"]]["xfm_corobl"].format( - **wildcards - ), - output: - sub_to_cor=bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="T1w", - to="corobl", - desc="affine", - type_="itk" - ), - container: - config["singularity"]["autotop"] - group: - "subj" - shell: - "c3d_affine_tool -itk {input.sub_to_std} -itk {params.std_to_cor} -mult -oitk {output}" - - -rule invert_template_xfm_itk2ras: - input: - xfm_ras=bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="T1w", - to="corobl", - desc="affine", - type_="itk" - ), - output: - xfm_ras=bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="T1w", - to="corobl", - desc="affineInverse", - type_="ras" - ), - container: - config["singularity"]["autotop"] - group: - "subj" - shell: - "c3d_affine_tool -itk {input} -inv -o {output}" - - -rule template_xfm_itk2ras: - input: - xfm_ras=bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="{native_modality}", - to="corobl", - desc="affine", - type_="itk" - ), - output: - xfm_ras=bids( - root=work, - datatype="warps", - **config["subj_wildcards"], - suffix="xfm.txt", - from_="{native_modality,T1w|T2w}", - to="corobl", - desc="affine", - type_="ras" - ), - container: - config["singularity"]["autotop"] - group: - "subj" - shell: - "c3d_affine_tool -itk {input} -o {output}" - - # apply transform to get subject in corobl cropped space rule warp_t1_to_corobl_crop: input: t1=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="preproc", suffix="T1w.nii.gz" ), xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T1w", to="corobl", @@ -298,7 +89,7 @@ rule warp_t1_to_corobl_crop: t1=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T1w.nii.gz", space="corobl", desc="preproc", @@ -318,7 +109,7 @@ rule lr_flip_t1: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T1w.nii.gz", space="corobl", desc="{desc}", @@ -328,7 +119,7 @@ rule lr_flip_t1: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T1w.nii.gz", space="corobl", desc="{desc}", diff --git a/hippunfold/workflow/rules/preproc_t2.smk b/hippunfold/workflow/rules/preproc_t2.smk index a05246a7..5b6b066a 100644 --- a/hippunfold/workflow/rules/preproc_t2.smk +++ b/hippunfold/workflow/rules/preproc_t2.smk @@ -1,12 +1,12 @@ rule import_t2: input: - config["input_path"]["T2w"], + inputs["T2w"].path, output: bids( root=work, datatype="anat", - **config["input_wildcards"]["T2w"], - suffix="T2w.nii.gz" + suffix="T2w.nii.gz", + **inputs["T2w"].wildcards, ), group: "subj" @@ -19,16 +19,16 @@ rule n4_t2: bids( root=work, datatype="anat", - **config["input_wildcards"]["T2w"], - suffix="T2w.nii.gz" + suffix="T2w.nii.gz", + **inputs["T2w"].wildcards, ), output: bids( root=work, datatype="anat", - **config["input_wildcards"]["T2w"], + desc="n4", suffix="T2w.nii.gz", - desc="n4" + **inputs["T2w"].wildcards, ), threads: 8 container: @@ -42,31 +42,36 @@ rule n4_t2: def get_ref_n4_t2(wildcards): # get the first image - t2_imgs = expand( - bids( - root=work, - datatype="anat", - **config["input_wildcards"]["T2w"], - suffix="T2w.nii.gz", - desc="n4" - ), - zip, - **snakebids.filter_list(config["input_zip_lists"]["T2w"], wildcards) + t2_imgs = ( + inputs["T2w"] + .filter(**wildcards) + .expand( + bids( + root=work, + datatype="anat", + desc="n4", + suffix="T2w.nii.gz", + **inputs["T2w"].wildcards, + ) + ) ) + return t2_imgs[0] def get_floating_n4_t2(wildcards): - t2_imgs = expand( - bids( - root=work, - datatype="anat", - **config["input_wildcards"]["T2w"], - suffix="T2w.nii.gz", - desc="n4" - ), - zip, - **snakebids.filter_list(config["input_zip_lists"]["T2w"], wildcards) + t2_imgs = ( + inputs["T2w"] + .filter(**wildcards) + .expand( + bids( + root=work, + datatype="anat", + suffix="T2w.nii.gz", + desc="n4", + **inputs["T2w"].wildcards, + ), + ) ) return t2_imgs[int(wildcards.idx)] @@ -79,7 +84,7 @@ rule reg_t2_to_ref: xfm_ras=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w{idx}", to="T2w0", @@ -89,7 +94,7 @@ rule reg_t2_to_ref: xfm_itk=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w{idx}", to="T2w0", @@ -99,10 +104,10 @@ rule reg_t2_to_ref: warped=bids( root=work, datatype="anat", - **config["subj_wildcards"], suffix="T2w.nii.gz", desc="aligned", - floating="{idx}" + floating="{idx}", + **inputs.subj_wildcards, ), container: config["singularity"]["autotop"] @@ -115,40 +120,38 @@ rule reg_t2_to_ref: def get_aligned_n4_t2(wildcards): # first get the number of floating t2s - filtered = snakebids.filter_list(config["input_zip_lists"]["T2w"], wildcards) - num_scans = len(filtered["subject"]) + num_scans = len(inputs["T2w"].filter(**wildcards).expand()) # then, return the path, expanding over range(1,num_scans) -i.e excludes 0 (ref image) - t2_imgs = expand( - bids( - root=work, - datatype="anat", - **config["subj_wildcards"], - suffix="T2w.nii.gz", - desc="aligned", - floating="{idx}" - ), - **wildcards, - idx=range(1, num_scans) + t2_imgs = ( + inputs["T2w"] + .filter(**wildcards) + .expand( + bids( + root=work, + datatype="anat", + desc="aligned", + floating="{idx}", + suffix="T2w.nii.gz", + **inputs.subj_wildcards, + ), + idx=range(1, num_scans), + ) ) return t2_imgs if config["skip_preproc"]: - # grabs the first t2w only + # for preproc T2, we expect the user to use bids filters/wildcards to ensure only 1 T1w is matched per subject rule import_preproc_t2: input: - lambda wildcards: expand( - config["input_path"]["T2w"], - zip, - **snakebids.filter_list(config["input_zip_lists"]["T2w"], wildcards) - )[0], + lambda wildcards: inputs["T2w"].filter(**wildcards).expand()[0], output: bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", desc="preproc" ), @@ -170,7 +173,7 @@ else: bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", desc="preproc" ), @@ -187,14 +190,14 @@ rule reg_t2_to_t1: flo=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", desc="preproc" ), ref=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="preproc", suffix="T1w.nii.gz" ), @@ -202,7 +205,7 @@ rule reg_t2_to_t1: warped=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", desc="preproc", space="T1w" @@ -210,7 +213,7 @@ rule reg_t2_to_t1: xfm_ras=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w", to="T1w", @@ -220,7 +223,7 @@ rule reg_t2_to_t1: xfm_itk=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w", to="T1w", @@ -230,7 +233,7 @@ rule reg_t2_to_t1: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="reg.txt", from_="T2w", to="T1w", @@ -254,7 +257,7 @@ def get_inputs_compose_t2_xfm_corobl(wildcards): bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w", to="T1w", @@ -266,7 +269,7 @@ def get_inputs_compose_t2_xfm_corobl(wildcards): bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T1w", to="corobl", @@ -282,7 +285,7 @@ def get_inputs_compose_t2_xfm_corobl(wildcards): bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w", to=config["template"], @@ -323,7 +326,7 @@ rule compose_t2_xfm_corobl: t2_to_cor=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w", to="corobl", @@ -333,7 +336,7 @@ rule compose_t2_xfm_corobl: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="composecorobl.txt", from_="T2w", to="corobl", @@ -354,7 +357,7 @@ def get_xfm_to_corobl(): xfm = bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T1w", to="corobl", @@ -366,7 +369,7 @@ def get_xfm_to_corobl(): bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w", to="corobl", @@ -383,7 +386,7 @@ rule warp_t2_to_corobl_crop: nii=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", desc="preproc" ), @@ -396,7 +399,7 @@ rule warp_t2_to_corobl_crop: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", space="corobl", desc="preproc", @@ -416,7 +419,7 @@ rule lr_flip_t2: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", space="corobl", desc="{desc}", @@ -426,7 +429,7 @@ rule lr_flip_t2: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", space="corobl", desc="{desc}", diff --git a/hippunfold/workflow/rules/qc.smk b/hippunfold/workflow/rules/qc.smk index 076fd9aa..6dbeb1ae 100644 --- a/hippunfold/workflow/rules/qc.smk +++ b/hippunfold/workflow/rules/qc.smk @@ -3,7 +3,7 @@ rule qc_reg_to_template: flo=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="{native_modality}.nii.gz", space=config["template"], desc="affine" @@ -21,7 +21,7 @@ rule qc_reg_to_template: bids( root=root, datatype="qc", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="regqc.png", from_="{native_modality}", to=config["template"] @@ -40,10 +40,10 @@ rule qc_reg_to_template: rule get_subfield_vols_subj: """Export segmentation volume for a subject to TSV""" input: - segs=expand( + segs=inputs[get_modality_key(config["modality"])].expand( bids( root=root, - **config["subj_wildcards"], + **inputs.subj_wildcards, datatype="anat", hemi="{hemi}", space="{crop_ref_spaces}", @@ -68,7 +68,7 @@ rule get_subfield_vols_subj: desc="subfields", atlas="{atlas}", suffix="volumes.tsv", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -85,7 +85,7 @@ rule plot_subj_subfields: desc="subfields", atlas="{atlas}", suffix="volumes.tsv", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: png=report( @@ -96,7 +96,7 @@ rule plot_subj_subfields: desc="subfields", atlas="{atlas}", suffix="volumes.png", - **config["subj_wildcards"] + **inputs.subj_wildcards ), caption="../report/subj_volume_plot.rst", category="Subfield Volumes", @@ -118,7 +118,7 @@ def get_bg_img_for_subfield_qc(wildcards): suffix="hippb500.nii.gz", space="{space}", hemi="{hemi}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ) elif config["modality"] == "cropseg": # blank image as bg @@ -128,7 +128,7 @@ def get_bg_img_for_subfield_qc(wildcards): suffix="cropref.nii.gz", space="{space}", hemi="{hemi}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ) elif config["modality"][:3] == "seg": @@ -140,7 +140,7 @@ def get_bg_img_for_subfield_qc(wildcards): suffix=f"{bg_modality}.nii.gz", space="{space}", hemi="{hemi}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ) else: @@ -152,7 +152,7 @@ def get_bg_img_for_subfield_qc(wildcards): suffix=f"{bg_modality}.nii.gz", space="{space}", hemi="{hemi}", - **config["subj_wildcards"], + **inputs.subj_wildcards, ) @@ -167,7 +167,7 @@ rule qc_subfield: space="{space}", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: png=report( @@ -179,7 +179,7 @@ rule qc_subfield: space="{space}", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), caption="../report/subfield_qc.rst", category="Segmentation QC", @@ -202,7 +202,7 @@ rule qc_subfield_surf: space="{ref_spaces}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: png=report( @@ -215,7 +215,7 @@ rule qc_subfield_surf: space="{ref_spaces}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), caption="../report/subfield_qc.rst", category="Segmentation QC", @@ -231,7 +231,7 @@ rule qc_subfield_surf: rule concat_subj_vols_tsv: """Concatenate all subject tsv files into a single tsv""" input: - tsv=lambda wildcards: expand( + tsv=lambda wildcards: inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="anat", @@ -239,12 +239,10 @@ rule concat_subj_vols_tsv: space="{space}", atlas="{atlas}", suffix="volumes.tsv", - **config["subj_wildcards"] + **inputs.subj_wildcards ), - subject=config["input_lists"][get_modality_key(config["modality"])][ - "subject" - ], - session=config["sessions"], + subject=inputs[get_modality_key(config["modality"])].zip_lists["subject"], + session=inputs[get_modality_key(config["modality"])].zip_lists["session"], space=wildcards.space, atlas=wildcards.atlas, ), diff --git a/hippunfold/workflow/rules/resample_final_to_crop_native.smk b/hippunfold/workflow/rules/resample_final_to_crop_native.smk index 417ae5ce..04e04ba2 100644 --- a/hippunfold/workflow/rules/resample_final_to_crop_native.smk +++ b/hippunfold/workflow/rules/resample_final_to_crop_native.smk @@ -2,7 +2,7 @@ rule create_native_crop_ref: """Create ref space for hires crop in native space TODO: expose the resampling factor and size as cmd line args""" input: - seg=expand( + seg=inputs[get_modality_key(config["modality"])].expand( bids( root=root, datatype="anat", @@ -11,7 +11,7 @@ rule create_native_crop_ref: space="{native_modality}", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), atlas=config["atlas"][0], allow_missing=True, @@ -26,7 +26,7 @@ rule create_native_crop_ref: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -41,7 +41,7 @@ rule resample_unet_native_crop: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="nnunet", space="corobl", @@ -50,7 +50,7 @@ rule resample_unet_native_crop: xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -63,7 +63,7 @@ rule resample_unet_native_crop: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: nii=bids( @@ -73,7 +73,7 @@ rule resample_unet_native_crop: desc="unet", space="crop{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -89,7 +89,7 @@ rule resample_postproc_native_crop: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="postproc", space="corobl", @@ -98,7 +98,7 @@ rule resample_postproc_native_crop: xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -111,7 +111,7 @@ rule resample_postproc_native_crop: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: nii=bids( @@ -121,7 +121,7 @@ rule resample_postproc_native_crop: desc="postproc", space="crop{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -142,12 +142,12 @@ rule resample_subfields_native_crop: space="corobl", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -160,7 +160,7 @@ rule resample_subfields_native_crop: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: nii=bids( @@ -171,7 +171,7 @@ rule resample_subfields_native_crop: space="crop{native_modality}", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -193,12 +193,12 @@ rule resample_coords_native_crop: desc="{desc}", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -211,7 +211,7 @@ rule resample_coords_native_crop: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: nii=bids( @@ -223,7 +223,7 @@ rule resample_coords_native_crop: space="crop{native_modality}", hemi="{hemi}", label="{autotop}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -239,7 +239,7 @@ rule resample_native_to_crop: nii=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="preproc", suffix="{native_modality}.nii.gz" ), @@ -249,7 +249,7 @@ rule resample_native_to_crop: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: nii=bids( @@ -259,7 +259,7 @@ rule resample_native_to_crop: suffix="{native_modality}.nii.gz", space="crop{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -277,7 +277,7 @@ def get_xfm_t2_to_t1(): xfm = bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="T2w", to="{native_modality}", @@ -292,7 +292,7 @@ rule resample_t2_to_crop: nii=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="T2w.nii.gz", desc="preproc" ), @@ -302,7 +302,7 @@ rule resample_t2_to_crop: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), xfm=get_xfm_t2_to_t1(), params: @@ -317,7 +317,7 @@ rule resample_t2_to_crop: suffix="T2w.nii.gz", space="crop{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] diff --git a/hippunfold/workflow/rules/shape_inject.smk b/hippunfold/workflow/rules/shape_inject.smk index f895d00f..2851fe7a 100644 --- a/hippunfold/workflow/rules/shape_inject.smk +++ b/hippunfold/workflow/rules/shape_inject.smk @@ -1,12 +1,45 @@ +# Template-based segmentation supports templates that have only a single hemisphere +# by mapping it to the flipped version of the other hemisphere. +# If a template has both L and R files, then we set hemi_constrained_wildcard to L|R. +# If a hemisphere is missing data, then we set it to flip that, e.g. if L missing, then use Lflip|R + +hemi_constraints = [] +if config["template"] in config["template_based_segmentation"]: + for hemi in config["hemi"]: + if hemi in config["template_based_segmentation"][config["template"]]["hemi"]: + hemi_constraints.append(hemi) + else: + hemi_constraints.append(f"{hemi}flip") + +hemi_constrained_wildcard = "{{hemi,{constraints}}}".format( + constraints="|".join(hemi_constraints) +) + + +def flipped(wildcards): + """function to map hemi in wildcards from Lflip to R, or Rflip to L, + for use in rules where e.g. the output wildcard is Lflip, but for the input, R is desired, such as + when mapping a R hemi dseg to the Lflip hemisphere of a subject.""" + + if wildcards.hemi == "L" or wildcards.hemi == "R": + return wildcards + elif wildcards.hemi == "Lflip": + wildcards.hemi = "R" + return wildcards + elif wildcards.hemi == "Rflip": + wildcards.hemi = "L" + return wildcard + + def get_input_for_shape_inject(wildcards): if config["modality"] == "cropseg": seg = bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) elif get_modality_key(config["modality"]) == "seg": modality_suffix = get_modality_suffix(config["modality"]) @@ -14,22 +47,22 @@ def get_input_for_shape_inject(wildcards): bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", space="corobl", hemi="{hemi}", - from_="{modality_suffix}" + from_="{modality_suffix}", ).format(**wildcards, modality_suffix=modality_suffix), ) else: seg = bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="nnunet", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) return seg @@ -39,10 +72,10 @@ def get_input_splitseg_for_shape_inject(wildcards): seg = bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dsegsplit", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) elif get_modality_key(config["modality"]) == "seg": @@ -50,21 +83,21 @@ def get_input_splitseg_for_shape_inject(wildcards): seg = bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dsegsplit", space="corobl", hemi="{hemi}", - from_="{modality_suffix}" + from_="{modality_suffix}", ).format(**wildcards, modality_suffix=modality_suffix) else: seg = bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dsegsplit", desc="nnunet", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) return seg @@ -92,15 +125,16 @@ rule import_template_shape: params: template_seg=lambda wildcards, input: Path(input.template_dir) / config["template_files"][config["inject_template"]]["dseg"].format( - **wildcards + **flipped(wildcards) ), output: template_seg=bids( root=work, datatype="anat", space="template", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="hipptissue", + hemi=hemi_constrained_wildcard, suffix="dseg.nii.gz" ), group: @@ -162,8 +196,9 @@ rule template_shape_reg: root=work, datatype="anat", space="template", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="hipptissue", + hemi="{hemi}", suffix="dsegsplit" ), subject_seg=get_input_splitseg_for_shape_inject, @@ -175,7 +210,7 @@ rule template_shape_reg: output: matrix=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", datatype="warps", desc="moments", @@ -183,18 +218,18 @@ rule template_shape_reg: to="subject", space="corobl", type_="ras", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="greedy", from_="template", to="subject", space="corobl", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -204,8 +239,8 @@ rule template_shape_reg: log: bids( root="logs", - **config["subj_wildcards"], - hemi="{hemi,Lflip|R}", + **inputs.subj_wildcards, + hemi=hemi_constrained_wildcard, suffix="templateshapereg.txt" ), shell: @@ -220,14 +255,15 @@ rule template_shape_inject: root=work, datatype="anat", space="template", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="hipptissue", + hemi="{hemi}", suffix="dseg.nii.gz" ), subject_seg=get_input_for_shape_inject, matrix=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", datatype="warps", desc="moments", @@ -235,18 +271,18 @@ rule template_shape_inject: to="subject", space="corobl", type_="ras", - hemi="{hemi}" + hemi="{hemi}", ), warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="greedy", from_="template", to="subject", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ), params: interp_opt="-ri LABEL 0.2vox", @@ -254,18 +290,18 @@ rule template_shape_inject: inject_seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="inject", space="corobl", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="templateshapeinject.txt", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -281,7 +317,7 @@ rule inject_init_laplace_coords: subject_seg=get_input_for_shape_inject, matrix=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", datatype="warps", desc="moments", @@ -289,18 +325,18 @@ rule inject_init_laplace_coords: to="subject", space="corobl", type_="ras", - hemi="{hemi}" + hemi="{hemi}", ), warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="greedy", from_="template", to="subject", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ), template_dir=Path(download_dir) / "template" / config["inject_template"], params: @@ -313,23 +349,23 @@ rule inject_init_laplace_coords: init_coords=bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="{autotop}", suffix="coords.nii.gz", desc="init", space="corobl", - hemi="{hemi,R|Lflip}" + hemi=hemi_constrained_wildcard, ), log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="{autotop}", suffix="injectcoords.txt", desc="init", - hemi="{hemi,R|Lflip}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -346,7 +382,7 @@ rule unflip_init_coords: nnunet_seg=bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="{autotop}", suffix="coords.nii.gz", @@ -359,13 +395,13 @@ rule unflip_init_coords: nnunet_seg=bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="{autotop}", suffix="coords.nii.gz", desc="init", space="corobl", - hemi="{hemi,L}" + hemi="{hemi,L|R}" ), container: config["singularity"]["autotop"] @@ -381,11 +417,11 @@ rule reinsert_subject_labels: inject_seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="inject", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ), subject_seg=get_input_for_shape_inject, params: @@ -396,11 +432,11 @@ rule reinsert_subject_labels: postproc_seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="postproc", space="corobl", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -419,7 +455,7 @@ rule unflip_postproc: desc="postproc", space="corobl", hemi="{hemi}flip", - **config["subj_wildcards"] + **inputs.subj_wildcards ), unflip_ref=get_input_for_shape_inject, output: @@ -429,8 +465,8 @@ rule unflip_postproc: suffix="dseg.nii.gz", desc="postproc", space="corobl", - hemi="{hemi,L}", - **config["subj_wildcards"] + hemi="{hemi,L|R}", + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] diff --git a/hippunfold/workflow/rules/subfields.smk b/hippunfold/workflow/rules/subfields.smk index 7a3397b6..229b5b87 100644 --- a/hippunfold/workflow/rules/subfields.smk +++ b/hippunfold/workflow/rules/subfields.smk @@ -9,11 +9,11 @@ rule resample_unfoldreg_subfields: hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN", @@ -32,7 +32,7 @@ rule resample_unfoldreg_subfields: hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -57,7 +57,7 @@ def skip_unfoldreg_option_subfields(wildcards): hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ) else: label_nii = bids( @@ -68,7 +68,7 @@ def skip_unfoldreg_option_subfields(wildcards): hemi="{hemi}", label="hipp", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ) return label_nii @@ -86,7 +86,7 @@ rule label_subfields_from_vol_coords_corobl: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), nii_pd=bids( root=work, @@ -97,7 +97,7 @@ rule label_subfields_from_vol_coords_corobl: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), nii_io=get_laminar_coords, labelmap=get_labels_for_laplace, @@ -112,7 +112,7 @@ rule label_subfields_from_vol_coords_corobl: space="corobl", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -154,7 +154,7 @@ rule combine_tissue_subfield_labels_corobl: space="corobl", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), params: remap=get_tissue_atlas_remapping, @@ -167,7 +167,7 @@ rule combine_tissue_subfield_labels_corobl: space="corobl", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -188,12 +188,12 @@ rule resample_subfields_to_native: space="corobl", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -203,7 +203,7 @@ rule resample_subfields_to_native: ref=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="preproc", suffix="{native_modality}.nii.gz" ), @@ -216,7 +216,7 @@ rule resample_subfields_to_native: space="{native_modality,T1w|T2w}", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -233,7 +233,7 @@ rule resample_postproc_to_native: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="postproc", space="corobl", @@ -242,7 +242,7 @@ rule resample_postproc_to_native: xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -252,7 +252,7 @@ rule resample_postproc_to_native: ref=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="preproc", suffix="{native_modality}.nii.gz" ), @@ -264,7 +264,7 @@ rule resample_postproc_to_native: desc="postproc", space="{native_modality,T2w|T2w}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -281,7 +281,7 @@ rule resample_unet_to_native: nii=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="nnunet", space="corobl", @@ -290,7 +290,7 @@ rule resample_unet_to_native: xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -300,7 +300,7 @@ rule resample_unet_to_native: ref=bids( root=root, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, desc="preproc", suffix="{native_modality}.nii.gz" ), @@ -312,7 +312,7 @@ rule resample_unet_to_native: desc="unet", space="{native_modality,T1w|T2w}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -334,12 +334,12 @@ rule resample_subfields_to_unfold: space="corobl", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), xfm=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", hemi="{hemi}", from_="corobl", @@ -355,7 +355,7 @@ rule resample_subfields_to_unfold: space="unfold", hemi="{hemi}", atlas="{atlas}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] diff --git a/hippunfold/workflow/rules/templateseg.smk b/hippunfold/workflow/rules/templateseg.smk index 8620f2a7..bbcbc4e9 100644 --- a/hippunfold/workflow/rules/templateseg.smk +++ b/hippunfold/workflow/rules/templateseg.smk @@ -45,7 +45,7 @@ rule template_reg: fixed_img=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="{modality}.nii.gz".format( modality=get_modality_suffix(config["modality"]) ), @@ -69,7 +69,7 @@ rule template_reg: output: warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="greedytemplatereg", @@ -94,7 +94,7 @@ rule warp_template_dseg: ref=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix=f"{config['modality']}.nii.gz", space="corobl", desc="preproc", @@ -102,7 +102,7 @@ rule warp_template_dseg: ), warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="greedytemplatereg", @@ -122,7 +122,7 @@ rule warp_template_dseg: inject_seg=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="dseg.nii.gz", desc="postproc", space="corobl", @@ -143,7 +143,7 @@ rule warp_template_coords: ref=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix=f"{config['modality']}.nii.gz", space="corobl", desc="preproc", @@ -151,7 +151,7 @@ rule warp_template_coords: ), warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="greedytemplatereg", @@ -170,7 +170,7 @@ rule warp_template_coords: init_coords=bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="{autotop}", suffix="coords.nii.gz", @@ -192,7 +192,7 @@ rule warp_template_anat: ref=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix=f"{config['modality']}.nii.gz", space="corobl", desc="preproc", @@ -200,7 +200,7 @@ rule warp_template_anat: ), warp=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="greedytemplatereg", @@ -223,7 +223,7 @@ rule warp_template_anat: warped=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix=f"{config['modality']}.nii.gz", desc="warpedtemplate", space="corobl", @@ -247,12 +247,12 @@ rule unflip_template_dseg: desc="postproc", space="corobl", hemi="{hemi}flip", - **config["subj_wildcards"] + **inputs.subj_wildcards ), unflip_ref=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix=f"{config['modality']}.nii.gz", space="corobl", desc="preproc", @@ -266,7 +266,7 @@ rule unflip_template_dseg: desc="postproc", space="corobl", hemi="{hemi,L|R}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), container: config["singularity"]["autotop"] @@ -282,7 +282,7 @@ rule unflip_template_coords: nii=bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="{autotop}", suffix="coords.nii.gz", @@ -293,7 +293,7 @@ rule unflip_template_coords: unflip_ref=bids( root=work, datatype="anat", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix=f"{config['modality']}.nii.gz", space="corobl", desc="preproc", @@ -303,7 +303,7 @@ rule unflip_template_coords: nii=bids( root=work, datatype="coords", - **config["subj_wildcards"], + **inputs.subj_wildcards, dir="{dir}", label="{autotop}", suffix="coords.nii.gz", diff --git a/hippunfold/workflow/rules/warps.smk b/hippunfold/workflow/rules/warps.smk index cbdd11d8..e2e62854 100644 --- a/hippunfold/workflow/rules/warps.smk +++ b/hippunfold/workflow/rules/warps.smk @@ -1,3 +1,201 @@ +def reg_to_template_cmd(wildcards, input, output): + ref = str( + Path(input.template_dir) + / config["template_files"][config["template"]][wildcards.modality].format( + **wildcards + ), + ) + if config["no_reg_template"]: + cmd = f"reg_resample -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {input.xfm_identity}; cp {input.xfm_identity} {output.xfm_ras}" + elif config["rigid_reg_template"]: + cmd = f"reg_aladin -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {output.xfm_ras} -rigOnly" + else: + cmd = f"reg_aladin -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {output.xfm_ras}" + return cmd + + +rule reg_to_template: + """ generic for T1w or T2w right now """ + input: + flo=bids( + root=root, + datatype="anat", + **inputs.subj_wildcards, + desc="preproc", + suffix="{modality}.nii.gz" + ), + xfm_identity=os.path.join(workflow.basedir, "..", config["xfm_identity"]), + template_dir=Path(download_dir) / "template" / config["template"], + params: + cmd=reg_to_template_cmd, + output: + warped_subj=bids( + root=work, + datatype="anat", + **inputs.subj_wildcards, + suffix="{modality,T1w|T2w}.nii.gz", + space=config["template"], + desc="affine" + ), + xfm_ras=bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="{modality,T1w|T2w}", + to=config["template"], + desc="affine", + type_="ras" + ), + log: + bids( + root="logs", + **inputs.subj_wildcards, + suffix="reg.txt", + from_="{modality,T1w|T2w}", + to=config["template"], + desc="affine", + type_="ras" + ), + container: + config["singularity"]["autotop"] + group: + "subj" + shell: + "{params.cmd}" + + +rule convert_template_xfm_ras2itk: + input: + bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="{reg_suffix}", + to=config["template"], + desc="affine", + type_="ras" + ), + output: + bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="{reg_suffix}", + to=config["template"], + desc="affine", + type_="itk" + ), + container: + config["singularity"]["autotop"] + group: + "subj" + shell: + "c3d_affine_tool {input} -oitk {output}" + + +# now have subject -> template transform, can compose that with template -> corobl to get subject -> corobl +rule compose_template_xfm_corobl: + input: + sub_to_std=bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="T1w", + to=config["template"], + desc="affine", + type_="itk" + ), + template_dir=Path(download_dir) / "template" / config["template"], + params: + std_to_cor=lambda wildcards, input: Path(input.template_dir) + / config["template_files"][config["template"]]["xfm_corobl"].format( + **wildcards + ), + output: + sub_to_cor=bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="T1w", + to="corobl", + desc="affine", + type_="itk" + ), + container: + config["singularity"]["autotop"] + group: + "subj" + shell: + "c3d_affine_tool -itk {input.sub_to_std} -itk {params.std_to_cor} -mult -oitk {output}" + + +rule invert_template_xfm_itk2ras: + input: + xfm_ras=bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="T1w", + to="corobl", + desc="affine", + type_="itk" + ), + output: + xfm_ras=bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="T1w", + to="corobl", + desc="affineInverse", + type_="ras" + ), + container: + config["singularity"]["autotop"] + group: + "subj" + shell: + "c3d_affine_tool -itk {input} -inv -o {output}" + + +rule template_xfm_itk2ras: + input: + xfm_ras=bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="{native_modality}", + to="corobl", + desc="affine", + type_="itk" + ), + output: + xfm_ras=bids( + root=work, + datatype="warps", + **inputs.subj_wildcards, + suffix="xfm.txt", + from_="{native_modality,T1w|T2w}", + to="corobl", + desc="affine", + type_="ras" + ), + container: + config["singularity"]["autotop"] + group: + "subj" + shell: + "c3d_affine_tool -itk {input} -o {output}" + + rule create_native_coord_ref: input: coords_ap=bids( @@ -9,7 +207,7 @@ rule create_native_coord_ref: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: nii=bids( @@ -19,7 +217,7 @@ rule create_native_coord_ref: hemi="{hemi}", label="{autotop}", suffix="refcoords.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -49,7 +247,7 @@ rule create_unfold_ref: label="{autotop}", datatype="warps", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -68,7 +266,7 @@ rule create_unfold_coord_map: label="{autotop}", datatype="warps", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: nii=bids( @@ -77,7 +275,7 @@ rule create_unfold_coord_map: space="unfold", label="{autotop}", suffix="refcoords.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), group: "subj" @@ -98,7 +296,7 @@ def get_laminar_coords(wildcards): desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ) elif "equivolume" in config["laminar_coords_method"]: coords_io = bids( @@ -110,7 +308,7 @@ def get_laminar_coords(wildcards): desc="equivol", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ) return coords_io @@ -123,7 +321,7 @@ rule create_warps_hipp: label="hipp", datatype="warps", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), unfold_phys_coords_nii=bids( root=work, @@ -131,7 +329,7 @@ rule create_warps_hipp: label="hipp", datatype="coords", suffix="refcoords.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), coords_ap=bids( root=work, @@ -142,7 +340,7 @@ rule create_warps_hipp: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), coords_pd=bids( root=work, @@ -153,7 +351,7 @@ rule create_warps_hipp: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), coords_io=get_laminar_coords, native_ref_coords_nii=bids( @@ -163,20 +361,18 @@ rule create_warps_hipp: hemi="{hemi}", label="hipp", suffix="refcoords.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), labelmap=get_labels_for_laplace, params: - interp_method="linear", gm_labels=lambda wildcards: config["laplace_labels"]["AP"]["gm"], - epsilon=lambda wildcards: config["unfold_crop_epsilon_fractions"], resources: mem_mb=16000, output: warp_unfold2native=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="hipp", suffix="xfm.nii.gz", hemi="{hemi}", @@ -187,7 +383,7 @@ rule create_warps_hipp: warp_native2unfold=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="hipp", suffix="xfm.nii.gz", hemi="{hemi}", @@ -198,7 +394,7 @@ rule create_warps_hipp: warpitk_unfold2native=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="hipp", suffix="xfm.nii.gz", hemi="{hemi}", @@ -209,7 +405,7 @@ rule create_warps_hipp: warpitk_native2unfold=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="hipp", suffix="xfm.nii.gz", hemi="{hemi}", @@ -222,7 +418,7 @@ rule create_warps_hipp: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, hemi="{hemi}", suffix="create_warps-hipp.txt" ), @@ -240,7 +436,7 @@ rule create_warps_dentate: label="dentate", datatype="warps", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), unfold_phys_coords_nii=bids( root=work, @@ -248,7 +444,7 @@ rule create_warps_dentate: label="dentate", datatype="coords", suffix="refcoords.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), coords_ap=bids( root=work, @@ -259,7 +455,7 @@ rule create_warps_dentate: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), coords_pd=bids( root=work, @@ -270,7 +466,7 @@ rule create_warps_dentate: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), coords_io=bids( root=work, @@ -281,7 +477,7 @@ rule create_warps_dentate: desc="laplace", space="corobl", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), native_ref_coords_nii=bids( root=work, @@ -290,20 +486,18 @@ rule create_warps_dentate: hemi="{hemi}", label="dentate", suffix="refcoords.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), labelmap=get_labels_for_laplace, params: - interp_method="linear", gm_labels=lambda wildcards: config["laplace_labels"]["PD"]["sink"], - epsilon=lambda wildcards: config["unfold_crop_epsilon_fractions"], resources: mem_mb=16000, output: warp_unfold2native=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="dentate", suffix="xfm.nii.gz", hemi="{hemi}", @@ -314,7 +508,7 @@ rule create_warps_dentate: warp_native2unfold=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="dentate", suffix="xfm.nii.gz", hemi="{hemi}", @@ -325,7 +519,7 @@ rule create_warps_dentate: warpitk_unfold2native=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="dentate", suffix="xfm.nii.gz", hemi="{hemi}", @@ -336,7 +530,7 @@ rule create_warps_dentate: warpitk_native2unfold=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="dentate", suffix="xfm.nii.gz", hemi="{hemi}", @@ -349,7 +543,7 @@ rule create_warps_dentate: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, hemi="{hemi}", suffix="create_warps-dentate.txt" ), @@ -364,7 +558,7 @@ rule expand_unfolded_warps: input: warp2d=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN", @@ -380,12 +574,12 @@ rule expand_unfolded_warps: label="hipp", datatype="coords", suffix="refcoords.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: warp3d=bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN3D", @@ -410,7 +604,7 @@ def get_unfold2unfoldatlas(wildcards): fn = ( bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN3D", @@ -431,7 +625,7 @@ rule compose_warps_native_to_unfold: corobl2unfold=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="xfm.nii.gz", hemi="{hemi}", @@ -445,12 +639,12 @@ rule compose_warps_native_to_unfold: label="{autotop}", datatype="warps", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), native2corobl=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -461,7 +655,7 @@ rule compose_warps_native_to_unfold: bids( root=root, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="xfm.nii.gz", hemi="{hemi}", @@ -472,7 +666,7 @@ rule compose_warps_native_to_unfold: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="composexfm.txt", hemi="{hemi}", @@ -495,7 +689,7 @@ def get_unfoldatlas2unfold(wildcards): fn = ( bids( root=work, - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.nii.gz", datatype="warps", desc="SyN3D", @@ -524,7 +718,7 @@ rule compose_warps_unfold_to_crop_native: unfold2corobl=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="xfm.nii.gz", hemi="{hemi}", @@ -538,12 +732,12 @@ rule compose_warps_unfold_to_crop_native: suffix="cropref.nii.gz", space="{native_modality}", hemi="{hemi}", - **config["subj_wildcards"] + **inputs.subj_wildcards ), native2corobl=bids( root=work, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, suffix="xfm.txt", from_="{native_modality}", to="corobl", @@ -556,13 +750,13 @@ rule compose_warps_unfold_to_crop_native: label="{autotop}", datatype="warps", suffix="refvol.nii.gz", - **config["subj_wildcards"] + **inputs.subj_wildcards ), output: unfold2cropnative=bids( root=root, datatype="warps", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="xfm.nii.gz", hemi="{hemi}", @@ -573,7 +767,7 @@ rule compose_warps_unfold_to_crop_native: log: bids( root="logs", - **config["subj_wildcards"], + **inputs.subj_wildcards, label="{autotop}", suffix="composexfm.txt", hemi="{hemi}", diff --git a/hippunfold/workflow/scripts/create_warps.py b/hippunfold/workflow/scripts/create_warps.py index 6562d753..6f9105d3 100644 --- a/hippunfold/workflow/scripts/create_warps.py +++ b/hippunfold/workflow/scripts/create_warps.py @@ -1,7 +1,7 @@ import nibabel as nib import numpy as np -from scipy.interpolate import griddata -from scipy.interpolate import NearestNDInterpolator +import naturalneighbor +from scipy.stats import zscore logfile = open(snakemake.log[0], "w") print(f"Start", file=logfile, flush=True) @@ -25,9 +25,6 @@ def summary(name, array): return -# params: -interp_method = snakemake.params.interp_method - # load unfolded coordinate map # unfold_ref_nib = nib.load(snakemake.input.unfold_ref_nii) unfold_phys_coords_nib = nib.load(snakemake.input.unfold_phys_coords_nii) @@ -66,7 +63,7 @@ def summary(name, array): # the unfolded space, using scipy's griddata (equivalent to matlab scatteredInterpolant). -coord_flat_ap = coord_ap[mask == True] # matlab: Laplace_AP = coord_ap(mask==1); +coord_flat_ap = coord_ap[mask == True] coord_flat_pd = coord_pd[mask == True] coord_flat_io = coord_io[mask == True] @@ -75,15 +72,11 @@ def summary(name, array): summary("coord_flat_io", coord_flat_io) # unravel indices of mask voxels into subscripts... -(i_L, j_L, k_L) = np.unravel_index( - idxgm, sz -) # matlab: [i_L,j_L,k_L]=ind2sub(sz,idxgm); +(i_L, j_L, k_L) = np.unravel_index(idxgm, sz) summary("i_L", i_L) # ... and stack into vectors ... -native_coords_mat = np.vstack( - (i_L, j_L, k_L, np.ones(i_L.shape)) -) # matlab: native_coords_mat = [i_L-1, j_L-1, k_L-1,ones(size(i_L))]'; +native_coords_mat = np.vstack((i_L, j_L, k_L, np.ones(i_L.shape))) summary("native_coords_mat", native_coords_mat) @@ -104,8 +97,6 @@ def summary(name, array): # scattered interpolation / griddata: -# matlab: interp_X = scatteredInterpolant(Laplace_AP,Laplace_PD,Laplace_IO,native_coords_phys(:,1),interp,extrap); - # we have points defined by coord_flat_{ap,pd,io}, and corresponding value as native_coords_phys[:,i] # and we want to interpolate on a grid in the unfolded space @@ -134,53 +125,27 @@ def summary(name, array): ), indexing="ij", ) +summary("points", points) -# tuple for use in griddata: -unfold_xi = (unfold_gx, unfold_gy, unfold_gz) -summary("unfold_gx", unfold_gx) -summary("unfold_gy", unfold_gy) -summary("unfold_gz", unfold_gz) - -# perform the interpolation, filling in outside values as 0 -# TODO: linear vs cubic? we were using "natural" interpolation in matlab -# so far, linear seems close enough.. -interp_ap = griddata( - points, values=native_coords_phys[:, 0], xi=unfold_xi, method=interp_method -) -summary("interp_ap", interp_ap) -interp_pd = griddata( - points, values=native_coords_phys[:, 1], xi=unfold_xi, method=interp_method -) -summary("interp_pd", interp_pd) -interp_io = griddata( - points, values=native_coords_phys[:, 2], xi=unfold_xi, method=interp_method -) -summary("interp_io", interp_ap) -# fill NaNs (NN interpolater allows for extrapolation!) -[x, y, z] = np.where(np.invert(np.isnan(interp_ap))) -interp = NearestNDInterpolator( - np.c_[x, y, z], interp_ap[np.invert(np.isnan(interp_ap))] -) -[qx, qy, qz] = np.where(np.isnan(interp_ap)) -fill = interp(qx, qy, qz) -interp_ap[np.isnan(interp_ap)] = fill +# perform the interpolation -[x, y, z] = np.where(np.invert(np.isnan(interp_pd))) -interp = NearestNDInterpolator( - np.c_[x, y, z], interp_pd[np.invert(np.isnan(interp_pd))] +interp_ap = naturalneighbor.griddata( + points, + native_coords_phys[:, 0], + [[0, unfold_dims[0], 1], [0, unfold_dims[1], 1], [0, unfold_dims[2], 1]], ) -[qx, qy, qz] = np.where(np.isnan(interp_pd)) -fill = interp(qx, qy, qz) -interp_pd[np.isnan(interp_pd)] = fill - -[x, y, z] = np.where(np.invert(np.isnan(interp_io))) -interp = NearestNDInterpolator( - np.c_[x, y, z], interp_io[np.invert(np.isnan(interp_io))] +interp_pd = naturalneighbor.griddata( + points, + native_coords_phys[:, 1], + [[0, unfold_dims[0], 1], [0, unfold_dims[1], 1], [0, unfold_dims[2], 1]], +) +interp_io = naturalneighbor.griddata( + points, + native_coords_phys[:, 2], + [[0, unfold_dims[0], 1], [0, unfold_dims[1], 1], [0, unfold_dims[2], 1]], ) -[qx, qy, qz] = np.where(np.isnan(interp_io)) -fill = interp(qx, qy, qz) -interp_io[np.isnan(interp_io)] = fill + # prepare maps for writing as warp file: @@ -189,10 +154,11 @@ def summary(name, array): mapToNative[:, :, :, 0, 0] = interp_ap mapToNative[:, :, :, 0, 1] = interp_pd mapToNative[:, :, :, 0, 2] = interp_io -# TODO: interpolate nans more better -mapToNative[np.isnan(mapToNative)] = 0 summary("mapToNative", mapToNative) +mapToNative[np.isnan(mapToNative)] = 0 + + # mapToNative has the absolute coordinates, but we want them relative to the # unfolded grid, so we subtract it out: displacementToNative = mapToNative - unfold_grid_phys @@ -228,13 +194,6 @@ def summary(name, array): # The image affine from the unfolded grid takes points from 0 to N to world coords, so # just need to un-normalize, then multiply by affine -# unnormalize -coord_flat_ap_unnorm = coord_flat_ap * unfold_dims[0] -coord_flat_pd_unnorm = coord_flat_pd * unfold_dims[1] -coord_flat_io_unnorm = coord_flat_io * unfold_dims[2] - -summary("coord_flat_ap_unnorm", coord_flat_ap_unnorm) - # reshape for multiplication (affine * vec) coord_flat_unnorm_vec = np.stack( @@ -259,7 +218,7 @@ def summary(name, array): summary("uvw_phys", uvw_phys) # now we have the absolute unfold world coords for each native grid point -# but we need the displacement from the native grid point world coord +# but we need the displacement from the native grid point world coord # the native world coords are in native_coords_phys # so we subtract it diff --git a/poetry.lock b/poetry.lock index c6075fa0..db77b3fd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,23 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} [[package]] name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category 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b/test_data/bids_T1w/dataset_description.json new file mode 100644 index 00000000..42b8aa44 --- /dev/null +++ b/test_data/bids_T1w/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test T1w Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/bids_T1w_longitudinal/dataset_description.json b/test_data/bids_T1w_longitudinal/dataset_description.json new file mode 100644 index 00000000..8f4a1953 --- /dev/null +++ b/test_data/bids_T1w_longitudinal/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test T1w longitudinal Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/bids_hippb500/dataset_description.json b/test_data/bids_hippb500/dataset_description.json new file mode 100644 index 00000000..ed093663 --- /dev/null +++ b/test_data/bids_hippb500/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test hippb500 Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/bids_multiT2w/dataset_description.json b/test_data/bids_multiT2w/dataset_description.json new file mode 100644 index 00000000..86b67067 --- /dev/null +++ b/test_data/bids_multiT2w/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test multi T2w Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/bids_segT2w/dataset_description.json b/test_data/bids_segT2w/dataset_description.json new file mode 100644 index 00000000..0b074a53 --- /dev/null +++ b/test_data/bids_segT2w/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test seg T2w Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/bids_singleT2w/dataset_description.json b/test_data/bids_singleT2w/dataset_description.json new file mode 100644 index 00000000..78ee3f7a --- /dev/null +++ b/test_data/bids_singleT2w/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test single T2w Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/bids_singleT2w_longitudinal/dataset_description.json b/test_data/bids_singleT2w_longitudinal/dataset_description.json new file mode 100644 index 00000000..38c60809 --- /dev/null +++ b/test_data/bids_singleT2w_longitudinal/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test single T2w longitudinal Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/data_cropseg/dataset_description.json b/test_data/data_cropseg/dataset_description.json new file mode 100644 index 00000000..988b7b6b --- /dev/null +++ b/test_data/data_cropseg/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test cropseg Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +} diff --git a/test_data/data_cropseg_1hemi/dataset_description.json b/test_data/data_cropseg_1hemi/dataset_description.json new file mode 100644 index 00000000..b3ab4d34 --- /dev/null +++ b/test_data/data_cropseg_1hemi/dataset_description.json @@ -0,0 +1,13 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": ["Peter Van Dyken", "Ali Khan", "Tristan Kuehn", "Jason Kai"], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test cropseg 1hemi Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/khanlab/snakebids", + "List of papers or websites" + ] +}