aomic-fc/code/yamls/PIOP2.yaml

workdir: /tmp

with:
  - junifer_extensions/parcellations/02_register_templateflow_schaefer_parcs.py
  - junifer_extensions/markers/smoothed_fc.py

datagrabber:
    kind: DataladAOMICPIOP2
    tasks: 
      - restingstate
      - emomatching
      - workingmemory

preprocess:
    kind: fMRIPrepConfoundRemover
    detrend: true
    standardize: true
    strategy:
        motion: full
        wm_csf: full
        global_signal: full
    low_pass: 0.08
    high_pass: 0.01
    masks:
      - inherit
      - compute_epi_mask
      - threshold: 0


markers:
  
  - name: parccortical-Schaefer100x17FSLMNI_parcsubcortical-TianxS2x3TxMNInonlinear2009cAsym_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: 
        - Schaefer100x17
        - TianxS2x3TxMNInonlinear2009cAsym
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
        
  - name: parccortical-Schaefer200x17FSLMNI_parcsubcortical-TianxS2x3TxMNInonlinear2009cAsym_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: 
        - Schaefer200x17
        - TianxS2x3TxMNInonlinear2009cAsym
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
  
  - name: parccortical-Schaefer400x17FSLMNI_parcsubcortical-TianxS2x3TxMNInonlinear2009cAsym_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: 
        - Schaefer400x17
        - TianxS2x3TxMNInonlinear2009cAsym
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit

  - name: parccortical-Schaefer100x17FSLMNI_parcsubcortical-TianxS2x3TxMNInonlinear2009cAsym_marker-smoothedFC
    kind: SmoothedFC
    fwhm: 6
    parcellation: 
        - Schaefer100x17
        - TianxS2x3TxMNInonlinear2009cAsym
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
        
  - name: parccortical-Schaefer200x17FSLMNI_parcsubcortical-TianxS2x3TxMNInonlinear2009cAsym_marker-smoothedFC
    kind: SmoothedFC
    fwhm: 6
    parcellation: 
        - Schaefer200x17
        - TianxS2x3TxMNInonlinear2009cAsym
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit
  
  - name: parccortical-Schaefer400x17FSLMNI_parcsubcortical-TianxS2x3TxMNInonlinear2009cAsym_marker-smoothedFC
    kind: SmoothedFC
    fwhm: 6
    parcellation: 
        - Schaefer400x17
        - TianxS2x3TxMNInonlinear2009cAsym
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit

  - name: parccortical-Schaefer400x17MNI152NLin2009cAsym_parcsubcortical-TianxS2x3TxMNInonlinear2009cAsym_marker-empiricalFC
    kind: FunctionalConnectivityParcels
    parcellation: 
        - Schaefer400x17_MNI152NLin2009cAsym
        - TianxS2x3TxMNInonlinear2009cAsym
    cor_method: correlation
    cor_method_params:
      empirical: true
    masks:
      - inherit

storage:
  kind: SQLiteFeatureStorage
  uri: ../../../junifer_storage/PIOP2/PIOP2

queue:
  jobname: PREPROCESS_PIOP2
  kind: HTCondor
  env:
    kind: conda
    name: junifer_release
  mem: 8G