ROI Extraction¶
clpipe comes with a variety of functional and anatomical atlases, which can be used to extract ROI time series data from functional scans.
Usage: fmri_roi_extraction [OPTIONS] [SUBJECTS]...
Options:
-config_file PATH Use a given configuration file. If left blank,
uses the default config file, requiring
definition of BIDS, working and output
directories. This will extract all ROI sets
specified in the configuration file.
-target_dir DIRECTORY Which postprocessed directory to process. If a
configuration file is provided with a target
directory, this argument is not necessary.
-target_suffix TEXT Which target suffix to process. If a
configuration file is provided with a target
suffix, this argument is not necessary.
-output_dir DIRECTORY Where to put the ROI extracted data. If a
configuration file is provided with a output
directory, this argument is not necessary.
-task TEXT Which task to process. If none, then all tasks
are processed.
-atlas_name TEXT What atlas to use. Please refer to documentation,
or use the command get_available_atlases to see
which are available. When specified for a custom
atlas, this is what the output files will be
named.
-custom_atlas TEXT A custom atlas image, in .nii or .nii.gz for
label or maps, or a .txt tab delimited set of ROI
coordinates if for a sphere atlas. Not needed if
specified in config.
-custom_label TEXT A custom atlas label file. Not needed if
specified in config.
-custom_type TEXT What type of atlas? (label, maps, or spheres).
Not needed if specified in config.
-radius TEXT If a sphere atlas, what radius sphere, in mm. Not
needed if specified in config.
-overlap_ok Are overlapping ROIs allowed?
-overwrite Overwrite existing files?
-log_output_dir DIRECTORY Where to put HPC output files (such as SLURM
output files). If not specified, defaults to
<outputDir>/batchOutput.
-submit Flag to submit commands to the HPC
-single Flag to directly run command. Used internally.
-debug Flag to enable detailed error messages and
traceback
--help Show this message and exit.
To view the available built-in atlases, you can use the get_available_atlases
command.
By default, ROIs are calculated with respect to the brain mask, and ROIs with fewer than the “PropVoxels” option voxels will be set to NAN. If any ROI has no voxels in the brain mask, then all ROIs will be extracted without respect to the brain mask, and then ROIs with fewer than “PropVoxels” voxels will be set to NAN. This is a workaround for the limitations on Nilearn’s ROI extractor functions.