results.cfg

A group-analysis definition file lists the source of data and configuration options for a General Linear Model group-level analysis.  

These files can be stored in [.cfg] or [.json] format.

Group-analysis definition files may have a combination of the following fields:

#data            : source of data

list of nifti files entered into second-level analysis (Nsubjects x Nmeasures) defining one or multiple outcome / dependent measures 

                                   note: when entering multiple files per subject (e.g. repeated measures) enter first all files (one per subject) for measure#1, followed by all files for measure#2, etc.

                                   note: NIFTI files may contain 3d volume-level data, fsaverage surface-level data, or ROI-to-ROI data (see conn_surf_write and conn_mtx_write to create surface/matrix nifti files)

  note: enter a single 4d file or a filename with wildcards (e.g. vol_*.nii) to simplify the specification of multiple files 

                                   alternatively list of SPM.mat files containing first-level analyses (Nsubjects x 1, or Nsubjects x Nmeasures)

                                   alternatively list of folder names containing SPM.mat first-level analyses (Nsubjects x 1, or Nsubjects x Nmeasures)

#design          : design matrix

(Neffects x Nsubjects) values defining different explanatory / independent measures or subject-effects 

enter one row for each modeled effect

each row should contain one value/number per subject

#contrast_between: between-subjects contrast

between-subjects contrast vector/matrix (Nc1 x Neffects) 

#contrast_within : within-subjects contrast 

within-subjects contrast vector/matrix (Nc2 x Nmeasures)

#contrast_names  : 1st-level contrast labels

(optional, only when entering SPM.mat files in #data field) list of contrast names to select from first-level analysis files (Nmeasures x 1)

#mask            : analysis mask

(optional) analysis-mask file

#analysistype    : analysis type

(optional) analysis type 1: include both parametric and non-parametric stats; 2: include only parametric stats (Random Field Theory assumptions); 3: include only non-parametric stats (permutation/randomization analyses)

#folder          :  output folder

(optional) folder where analysis are stored; default current folder

#data_labels     : data labels 

(optional) labels of columns of data matrix (for display purposes)

#design_labels   : design labels

(optional) labels of columns of design matrix (for display purposes)

#design_file     : design file

(optional) (alternative to design_matrix field) file containing design_matrix data (.csv/.tsv/.txt/.json/.mat with Nsubjects x Neffects matrix of explanatory / independent measures)

#design_matrix   :  (alternative format) design matrix

(Nsubjects x Neffects) values defining different explanatory / independent measures or subject-effects 

                                   enter one row for each subject

                                   each row should contain one value/number per modeled effect/covariate

analysis.cfg example:

#data

/data/beta_sub*.nii

/data/beta_sub02.nii

/data/beta_sub03.nii

/data/beta_sub04.nii

/data/beta_sub05.nii

/data/beta_sub06.nii

/data/beta_sub07.nii

/data/beta_sub08.nii

/data/beta_sub09.nii

/data/beta_sub10.nii

/data/beta_sub11.nii

/data/beta_sub12.nii

/data/beta_sub13.nii

#design

1 1 1 1 1 1 1 0 0 0 0 0 0

0 0 0 0 0 0 0 1 1 1 1 1 1

#contrast_between

-1 1

#folder

/data/analysis01