caps.functional_connectivity.setup.Setup¶
Setup¶
Inputs¶
[Mandatory]
anatomical_paths: a legal value (mandatory)
paths to all subjects anatomical directories
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anatomicals: a legal value (mandatory)
the anatomical files
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anatomicals_from_spreproc: a legal value (mandatory)
the spatially preprocessed anatomical files, output from conn
spatial preproc pipiline
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conditions_durations: a legal value (mandatory)
Conditon durations
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conditions_names: a legal value (mandatory)
Conditon names
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conditions_onsets: a legal value (mandatory)
Conditon onsets
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functional_paths: a legal value (mandatory)
paths to all subjects functional directories
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functionals: a legal value (mandatory)
the functional files
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functionals_from_spreproc: a legal value (mandatory)
the spatially preprocessed functional files, output from conn
spatial preprocessing pipiline
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nconditions: an integer (mandatory)
number of conditons
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nsubjects: an integer (mandatory)
Number of subjects
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rois_regresscovariates: a legal value (mandatory)
Regress out covariates, default to 1 for more than one dimension
extracted
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sp_anatomical_prefix: a string (mandatory)
the prefix of the spatially preprocessed anatomical images
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sp_functional_prefixes: a legal value (mandatory)
the prefixes of the spatially preprocessed functional images
associated to the sessions to include
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[Optional]
CSF_masks_prefix: a string (optional)
the prefix of spatially preprocessed CSF masks
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Grey_masks_prefix: a string (optional)
the prefix of spatially preprocessed Grey masks
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White_masks_prefix: a string (optional)
the prefix of spatially preprocessed White masks
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analysis: any value (optional)
Vector of index to analysis types (1: ROI-to-ROI; 2: Seed-to-
voxel; 3: Voxel-to-voxel) [1,2]
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covariates_files: a legal value (optional)
covariates files
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covariates_names: a legal value (optional)
covariates names
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covariates_prefixes: a legal value (optional)
the prefixes of covariates files for all sessions, of length
number of covariates
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done: an integer (optional)
1/0, [0]. 0: only edits project fields (do not run Setup->’Done’);
1: run Setup->’Done’
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isnew: an integer (optional)
1/0 is this a new conn project [0]
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masks_CSF_dimensions: an integer (optional)
Number of PCA components extracted from the csf matter [16]
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masks_CSF_files: a legal value (optional)
CSF mask volume file [defaults to CSF mask extracted from
structural volume]
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masks_Grey_dimensions: an integer (optional)
Number of PCA components extracted from the grey matter [1]
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masks_Grey_files: a legal value (optional)
grey matter mask volume file [defaults to Grey mask extracted from
structural volume]
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masks_White_dimensions: an integer (optional)
Number of PCA components extracted from the white matter [16]
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masks_White_files: a legal value (optional)
white matter mask volume file [defaults to White mask extracted
from structural volume]
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normalized: an integer (optional)
1/0 are the spatially preprocessed images normalizedor not
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overwrite: a legal value (optional)
overwrite existing results if they exist [‘Yes’]
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rois_dimensions: a legal value (optional)
number of dimensions characterizing each ROI activation. (1
represents only the mean BOLD activity within the ROI; 2 and above
includes additional PCA [1]
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rois_files: a legal value (optional)
List of ROIs files
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rois_mask: a legal value (optional)
Mask with Grey Matter [0]
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rois_multiplelabels: a legal value (optional)
Multiple ROIs, default to 1 for .nii or .img ROI files if
associated .txt or .csv or .xls files exist
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rois_names: a legal value (optional)
ROIs names, default to ROIs files
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t_r: a float (optional)
Repetition time (seconds) [2]
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Outputs¶
conn_batch: a legal value
the generated conn batch
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setup_dict: a legal value
dictionary with all conn setup parameters
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