T1Prep/T1Prep_defaults.txt at main · ChristianGaser/T1Prep · GitHub

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# ------------------------------------------------------------------------------
# General options
# ------------------------------------------------------------------------------
re_install=0          # Remove the existing installation and reinstall the
                      # required Python libraries
multi=-1              # Set the number of processes for parallelization. Use '-1'
                      # to automatically detect the number of available processors
min_memory=10         # Set the minimum memory size in GB for each process to be
                      # parallelized
debug=0               # Enable verbose output, retain temporary files, and save
                      # additional debugging information
retry=0               # Retry failed processing once (1=on, 0=off)

# ------------------------------------------------------------------------------
# Save options
# ------------------------------------------------------------------------------
nii_ext='nii'         # Define extension (nii.gz or nii)
save_h5=0             # Additionally save deformations as ANTs/ITK .h5
fmriprep=0            # Additionally save fMRIPrep-compatible results
estimate_surf=1       # Run surface and thickness estimation
estimate_seg=1        # Run segmentation processing
estimate_spherereg=1  # Run spherical surface registration
save_pial_white=1     # Additionally estimate pial and white matter surface
                      # during surface estimatio
save_lesions=0        # Additionally save WMH lesions
save_hemi=0           # Additionally save hemispheric partitions of the segmentation
save_csf=0            # Additionally save CSF segmentations
save_mwp=1            # Estimate modulated and warped segmentations
save_wp=0             # Additionally save warped segmentations
save_rp=0             # Additionally save affine-registered segmentations
save_p=0              # Additionally save native space segmentations
use_bids_naming=0     # Use BIDS standard for output file naming conventions
atlas_vol="'neuromorphometrics', 'cobra'"
                      # Define an atlas list in the format "'suit','cobra'"
atlas_surf="'aparc_DK40.freesurfer','aparc_a2009s.freesurfer'"
                      # Define an surface atlas list in the format
                      #"'aparc_DK40.freesurfer','aparc_a2009s.freesurfer'"

# ------------------------------------------------------------------------------
# Expert options
# ------------------------------------------------------------------------------
track=1               # Collect telemetry information for T1Prep
use_amap=0            # Use AMAP instead of DeepMRIPrep for segmentation
thickness_method=3    # Set the thickness method
correct_folding=1     # Correct for cortical thickness by folding effects
pre_fwhm=2            # Set the pre-smoothing FWHM size in CAT_VolMarchingCubes
vessel=1              # Use vessel removal
median_filter=2       # Set the number of median filter applications to reduce
                      # topology artefacts
fast=0                # Skip spherical registration and estimating atlases and
                      # warped segmentations