subject.cfg /.json

A subject definition file lists the original/raw data associated with an individual subject.  

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

Subject definition files may have a combination of the following fields:

#functionals : list of functional files, if appropriate

                        enter only one file per run/session

                        if starting from NIFTI files, enter here the functional files (e.g. /mydata/nii/984000-7.nii)

                        if starting from DICOM files (see 'dicoms' field below), enter here the runs that contain functional data

                            files may be specified by DICOM series numbers (e.g. entering 7 identifies files named *-7.nii output by the dicom converter step)

                            files may be specified by filenames without extension (e.g. entering 984000-7 identifies the 984000-7.nii files generated from 984000-7-*.dcm files)

                            enter simply * to indicate all DICOM series

                            enter simply ? (or do not include the 'functionals' field) to let users select functional files interactively (GUI)

#structurals: list of structural files, if appropriate

                        enter either a single file (for session-invariant structurals) or one file per run (for session-specific structurals)

                        if starting from NIFTI files, enter here the functional files (e.g. /mydata/nii/984000-3.nii)

                        if starting from DICOM files (see 'dicoms' field below), enter here the filenames/runs that contain structural data

                            files may be specified by DICOM series numbers (e.g. entering 3 identifies files named *-3.nii output by the dicom converter step)

                            files may be specified by filenames without extension (e.g. 984000-3)

                            enter simply * to indicate all DICOM series

                            enter simply ? to let user select functional files interactively (GUI)

#dicoms: list of dicom files, if appropriate

                            for <root>-<slice#>.dcm file naming convention: enter one file per run (only first file -1.dcm from each dicom series); output files will be named <root>.nii

                            for other file naming conventions: enter all dicom files; output files will be broken down by DICOM series and renamed as run-<series#>.nii

                        files may be specified explicitly (e.g. /mydata/dicoms/984000-1-1.dcm)

                        files may also include wildcards (e.g. /mydata/dicoms/*-1.dcm)

#vdm_functionals: list if voxel-displacement maps, if appropriate (for preprocessing.steps=='functional_realign&unwarp&phasemap')

                        enter a single file or one file per run/session (vdm* file; explicitly entering these volumes here superceeds CONN's 

                        default option to search for/use vdm* files in same directory as functional data) 

#fmap_functionals: list if fieldmap volumes, if appropriate (for preprocessing.steps=='functional_vdm_create')

                        enter either a) magnitude1+phasediff images; b) real1+imag1+real2+imag2; or c) fieldmap (in Hz) fieldmap acquisition sequence volumes

                        (note: use fmap_functionals_ss fieldname if entering session/run-specific sets of fieldmap files)

#rois.[roiname] : list of ROI files if appropriate

                        enter a single file or one file per run/session

for additional ROI details use fields: #rois.[roiname].files, #rois.[roiname].dimensions, #rois.[roiname].mask, #rois.[roiname].weighted, 

and #rois.[roiname].dataset (see help conn_batch Setup.rois section for details)

#RT: repetition time of functional data in seconds

#functionals_path: (when entering nifti files as functionals) folder where nifti files are stored [default: full paths are explicitly defined in functionals field]

#structurals_path: (when entering nifti files as structurals) folder where dicom files are stored [default: full paths are explicitly defined in structurals field]

#rois_path: (when entering nifti files as rois) folder where roi files are stored [default: full paths are explicitly defined in rois field]

#dicoms_path: (when entering dicom files as structurals and/or functionals) folder where dicom files are stored [full paths are explicitly defined in dicoms field]

#dicoms_outputfolder: (when entering dicom files as structurals and/or functionals) folder where nii files are stored (see 'folderout' options in conn_dcm2nii)  ['../nii']

#dicoms_outputoverwrite: (when entering dicom files as structurals and/or functionals) 1/0 overwrite existing .nii files if they exist [0]

data.cfg example:

#functionals

/Volumes/ext/SUBJECTS/subject0001/raw/func_01.nii

/Volumes/ext/SUBJECTS/subject0001/raw/func_02.nii

#structurals

/Volumes/ext/SUBJECTS/subject0001/raw/anat_01.nii

#RT

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