Functional configuration¶
general step¶
- fslRootDir
- default
"/Applications/fsl/5.0.10"- description
FSL home directory.
- freesurferRootDir
- default
"/Applications/freesurfer/6.0.0"- description
Freesurfer home directory.
- parameterPropertiesFile
- default
"functionalParameterProperties.xlsx"- description
Datasheet with overview, requirements and descriptions of CATO parameters.
- templates
- default
["aparc","economo","BB50human","lausanne120","lausanne250"]- description
List of parcellation templates used to reconstruct connectivity matrices and region properties.
- reconstructionSteps
- default
["functional_preprocessing","parcellation","collect_region_properties","compute_motion_metrics","reconstruction_functional_network"]- description
List of pipeline steps that will be executed.
- freesurferDir
- default
"T1/SUBJECT_FS"- description
Directory with output files of Freesurfer’s recon-all function.
- templatesDir
- default
"TOOLBOXDIR/templates"- description
Directory with template directories.
- ROIsFile
- default
"TEMPLATESDIR/TEMPLATE/ROIs_TEMPLATE.txt"- description
File with on each line region codes (as defined by the lookup table) that define the nodes (and order of nodes) corresponding to the regions in the output connectivity matrices and region properties.
- outputDir
- default
"fMRI_processed"- description
Output directory in which all generated files are stored (except additional Freesurfer files that are saved in the subject’s Freesurfer directory).
- logFile
- default
"OUTPUTDIR/functional_pipeline.log"- description
Log file. In case of consecutive runs the file will be appended.
- statusFile
- default
"OUTPUTDIR/functional_pipeline.STATUS"- description
Status file describing progress of CATO. Steps are either in “running”, “error” or “finished” state.
- computedConfigFile
- default
"OUTPUTDIR/functional_configuration.json"- description
File with configuration parameters that were effectively used in processing a subject.
- maxNumberCompThreads
- default
1- description
Maximum number of computational threads used in pipeline. Value 0 lets MATLAB determine the most desirable number of computational threads (equal to the number of physical cores on the machine).
functional_preprocessing step¶
- fmriFile
- default
"fMRI/SUBJECT_fmri.nii.gz"- description
Input fMRI file.
- fmriProcessedFile
- default
"OUTPUTDIR/SUBJECT_fmri.nii.gz"- description
Pre-processed fMRI file.
- motionParametersFile
- default
"OUTPUTDIR/SUBJECT_motion_parameters.par"- description
Motion parameters file. The format is expected to be like a motion parameters file created by MCFLIRT.
- fmriReferenceFile
- default
"OUTPUTDIR/SUBJECT_ref.nii.gz"- description
Reference file to which fMRI data is registered.
- registrationMatrixFile
- default
"OUTPUTDIR/SUBJECT_ref_to_freesurfer.dat"- description
Registration matrix describing the transform between the fmriReferenceFile and Freesurfer space (as created by bbregister).
- segmentationFile
- default
"OUTPUTDIR/SUBJECT_aseg_ref.nii.gz"- description
Freesurfer segmentation in fMRI space. The segmentation is mapped from Freesurfer to fMRI space using mri_label2vol with the registration matrix (from registrationMatrixFile) as input.
- sliceTimingCorrection
- default
true- description
Flag whether slice timing should be corrected (using FSL sliceTimer).
- sliceTimerOptions
- default
""- description
Optional input arguments for FSL slicetimer. The example preprocessing script executes the following code: “slicetimer -i fmriFileInput -o fmriFileOutput sliceTimerOptions”.
- fmriInfo
- default
""- description
Adjust variables in the fmriProcessedFile header (using mri_convert). Options are provided as structure (e.g. fmriInfo:{“tr”: TR in msec, “te”: TE in msec}). If emtpy, header is not changed.
- preprocessingScript
- default
"TOOLBOXDIR/functional_preprocessing/preprocess_default.sh"- description
Bash script that will be executed to run pre-processing on the input data.
parcellation step¶
- forceFreesurferOverwrite
- default
false- description
Flag whether the parcellation step should overwrite (if set to TRUE) already existing Freesurfer files.
- parcellationFile
- default
"OUTPUTDIR/SUBJECT_TEMPLATE+aseg_ref.nii.gz"- description
Parcellation of the fmriReferenceFile for each of the applied templates.
- templateScript
- default
"TEMPLATESDIR/TEMPLATE/parcellate_TEMPLATE.sh"- description
Bash script that performs parcellation steps.
- matchROIs
- default
true- description
Flag whether the parcellation step should reassign the ROIs in the parcellationFile to match the template’s color lookup table.
- lutFile
- default
"TEMPLATESDIR/TEMPLATE/TEMPLATE.annot.ctab"- description
Freesurfer’s color lookup table of the template.
collect_region_properties step¶
- statsLhFile
- default
"FREESURFERDIR/stats/lh.TEMPLATE.stats"- description
Freesurfer’s left-hemisphere stats file.
- statsRhFile
- default
"FREESURFERDIR/stats/rh.TEMPLATE.stats"- description
Freesurfer’s right-hemisphere stats file.
- statsSubFile
- default
"FREESURFERDIR/stats/aseg.stats"- description
Freesurfer’s subcortical stats file.
- regionPropertiesFile
- default
"OUTPUTDIR/SUBJECT_region_properties_TEMPLATE.mat"- description
MATLAB file including region properties (center of mass of each region, the number of vertices, surface area mm2, gray matter volume mm3, average thickness mm for each region in the ROIsFile.
compute_motion_metrics step¶
- motionMetricsFile
- default
"OUTPUTDIR/SUBJECT_motion_metrics.mat"- description
MATLAB file with motion metrics (DVARS and FD).
reconstruction_functional_network step¶
- methodDescription
- default
"scrubbed_0.01-0.1"- description
Name of reconstruction method. Can be referenced in other parameters with METHOD.
- reconstructionMethod
- default
"corr"- description
Functional connectivity estimation method used.
- connectivityMatrixFile
- default
"OUTPUTDIR/SUBJECT_connectivity_METHOD_TEMPLATE.mat"- description
MATLAB file with connectivity matrices for the used reconstruction methods and templates. File includes variables: weightDescriptions, ROIs, regionDescriptions, connectivity. ROIs is a list of the segmentation codes of the regions included in the connectivity matrix. regionDescriptions is a list of the names of the regions included in the connectivity matrix. weightDescriptions is a list of the measures by which connections are weighted in the connectivity matrix. Connectivity is a Nregion x Nregion x Nweighting variable that contains the connectivity matrices for all weightings.
- timeSeriesFile
- default
"OUTPUTDIR/SUBJECT_time_series_METHOD_TEMPLATE.mat"- description
MATLAB file with time series for the used reconstruction methods and templates.
- minRepetitionTime
- default
100- description
Repetition times smaller than minRepetitionTime are considered erros. This provides a check avoid issues due to different time measures (seconds versus milliseconds).
- regression.regressionMask
- default
[24,2,41,251,252,253,254,255]- description
List of FreeSurfer region codes (from the standard segmentation map, aseg.mgz) of voxels that will be used as regressor. The average signal of voxels for each region code is included as a regressor.
- regression.globalMeanRegression
- default
false- description
Flag whether global signal regression should be performed.
- bandpass_filter.filter
- default
true- description
Flag whether bandpass filtering should be performed.
- bandpass_filter.frequencies
- default
[0.01,0.1]- description
High- and low-pass frequencies.
- scrubbing.scrubbing
- default
true- description
Flag whether scrubbing should be performed.
- scrubbing.maxFD
- default
0.25- description
Frames with FD higher than maxFD are indicated to contain a violation.
- scrubbing.maxDVARS
- default
1.5- description
Frames with DVARS larger than Q3 + maxDVARS × IQR are indicated to contain a violation.
- scrubbing.minViolations
- default
2- description
Frames with a number of violations larger or equal to minViolations are considered to contain motion artifacts and scrubbed from further analyses.
- scrubbing.backwardNeighbors
- default
1- description
Number of frames preceding a violating-frame that are also excluded from analyses.
- scrubbing.forwardNeighbors
- default
0- description
Number of frames succeeding a violating-frame that are also excluded from analyses.
- saveTimeSeries
- default
true- description
Flag indicating whether time series are saved to timeSeriesFile.